Moola Vedas or Moola Veda is a concept expounded by Sri Madhvacharya. As per the Dvaita school of teaching in the Kruta Yuga (Satya Yuga – the first age as per Hinduism), the entire corpus of the Vedas including the Pancharatra used to be in merged form without any no internal classification such as Rig Veda, Yajur Veda etc. The entire corpus was collectively called as Moola Veda. As the knowledge of the people of that age was in the purest form, all Vedic names viz., Brahma, Indra, Rudra, Varuna were popular as the names of Bhagavan Vishnu Himself. Hence in various sacrifices propitiating Indra, Rudra, Brahma, Varuna and others, it was only Bhagavan Vishnu who was referred to and propitiated by all these names. The respective celestials became popular with such names much later only after the commencement of the Treta Yuga. In fact, in the Kruta Yuga, they used to be honored not as the deities but only as Manus - the visionaries or the chanters of the Vedic Mantras and inspirers of the Vishnu sacrifices. Hence there was no classification of the knowledge as Para Vidya or Apara Vidya. The entire corpus was considered as Para Vidya.
After the commencement of the Treta Yuga, such purity of
knowledge was not commonly available. As the knowledge began to depreciate,
some, though not all, were unable to worship Bhagavan Sri Hari Vishnu through
the Moola Vedas. Such people were allowed to worship Him through the individual
Vedas and the Pancharatra Agama. Hence, in the Treta Yuga, the Vedas became
three-fold and the other celestials also came to be popularly referred through
the Vedas. People also began to perform sacrifices to propitiate deities other
than Bhagavan Vishnu.
After the advent of the Dvapara Yuga, as the knowledge began
to depreciate further, some, though not all, were unable worship Vishnu as per
the Vedas. Such people were allowed to worship Bhagavan Vishnu through the
Pancharatra Agama. In the Kali Yuga, the knowledge will further depreciate and
those who lose the qualification to worship as prescribed in the Vedas or the
Pancharatra, Bhagavan is worshipped only by names.