Vajrayoginī is depicted treading on the breast of Kalarati, the principal worldly goddess with her right leg, whereas with her left leg, she treads on the forehead of black Bhairava, or wrathful Ishvara, the principal worldly god. Kalarati and Bhairavaaren’t the actual sentient beings, but manifestations of Vajrayoginī's wisdom of bliss and emptiness. They symbolize the maras of the delusions. Vajrayoginī treads on them to demonstrate that she has overcome attachment, hatred, and ignorance and to show that she is free from the fears of samsara (the cycle of life and death) and solitary peace. And thus, she can lead all sentient beings to the same freedom.

Vajrayoginī is depicted naked, with her breasts full and aroused, showing that she experiences great bliss and that she bestows the siddhi of great bliss upon her practitioners.   

Her brilliant red body symbolizes her inner fire, representing spontaneous bliss that overcomes the two obstructions: emotional obscurations (Kleshavarana) like anger and attachment that hinder liberation, and cognitive obscurations that block the realization of ultimate reality.  

Her three eyes signify her ability to perceive beyond the past, present, and future.    

By gazing upward towards the Pure Dakini Land, she demonstrates and guides her followers to enlightenment.   

In her right hand, Vajrayoginī, holds a curved knife, known as a Kartari, representing her ability to cut through the delusions and obstacles faced by her followers and all sentient beings.  

In her left hand, she holds Kapala, skull filled with blood, which symbolizes her experiencing bliss.  

Vajrayoginī's left shoulder supports a khatvanga, showing that she is never separated from her consort, Heruka. The khatvanga is Heruka himself, and the various features of the khatvanga represent various features and deities of Heruka's mandala.

The khatvanga is octagonal in cross-section, symbolizing the eight great charnel grounds of Heruka's mandala.   

At its lower tip, there is a single-pronged vajra, which symbolizes the protection circle of Heruka's mandala.   

Towards the upper end of the Katanga, there is a vase symbolizing Heruka's celestial mansion.  

Above this, there is a crossed vajra symbolizing the eight Deities of the commitment wheel who guard and maintain the sacred vows of Vajrayana practitioners.  

A freshly severed human head symbolizing the sixteen Deities of the heart wheel, the Niramanakaya embodying the wisdom aspect of enlightenment, perfect clarity and realization (purifies thoughts and deep realization).  

A rotting human head symbolizes the sixteen Deities of the speech wheel, the Sambhogakaya, which transforms ordinary speech into enlightened mantra and compassionate communication (purifies communication and mantra recitation).  

A bleached skull symbolizing the sixteen Deities of the body wheel, the Dharmakaya, which purify gross and subtle body energy, leading to pure, enlightened appearance (purifies physical actions).  

At the very top of the khatvanga, there is a five-pronged vajra symbolizing the five Deities of the great bliss wheel, representing the innermost, highest level of Heruka mandala. The Five Deities represent the final stage of awakening, where Vajrayoginī and Heruka guide the practitioner to the inseparable union of wisdom and bliss.  

Khatvanga is adorned with an elaborate scarf with two furls, representing the inseparability of the Mahayana and Vajrayana teachings.  

Vajrayoginī's five bone ornaments, also known as mudra-ornaments, symbolize the five perfections (pāramitās) of all Buddhas. These ornaments are made of human bone, signifying the transformation of death, impermanence, and worldly illusions into enlightened qualities.  

Vajrayoginī's five bone ornaments symbolize the five perfections (pāramitās) of all Buddhas.  

The five Buddhas corresponding to Vajrayoginī's bone ornaments and the five perfections are: Akshobhya (Meditative Concentration – Crown), Ratnasambhava (Patience – Ear), Vairocana (Mental Stabilization – Heart), Amoghasiddhi (Perseverance – Belt), and Amitābha (Moral Discipline – Arm and Leg). 

Her hair is black, symbolizing the unchangeable nature of her Truth Body. It falls freely down her back to show that she is free from the fetters of self-grasping. In the long dedication prayer of the sadhana, her hair is described as orange, but this refers mainly to her human emanations, who have appeared with orange hair, as witnessed by TsarchenLosal Gyatso and others.

Vajrayoginī’s fifty purified inner winds, which serve as the seeds of speech, are symbolized by her garland of fifty human skulls, representing the transformation of ordinary energies into enlightened speech and the fifty syllables of the Sanskrit alphabet, embodying the pure expression of ultimate wisdom.