Due to the unique electrical and mechanical properties of boron nitride nanotubes (BNNT), BNNT has been a promising material for many potential applications, especially in biomedical field. Understanding the dispersion of BNNT in aqueous solution by biomolecules is essential for its use in biomedical applications. In this study, BNNT wrapped by polynucleotides in aqueous solution was investigated by molecular dynamics (MD) simulations. Our results demonstrated that the BNNT wrapped by polynucleotides could greatly hinder the aggregation of BNNTs and improve the dispersion of BNNTs in aqueous solution. Dispersion of BNNTs with the assistance of polynucleotides is greatly affected by the wrapping manner of polynucleotides on BNNT, which mainly depends on two factors: the type of polynucleotides and the radius of BNNT. The interaction between polynucleotides and BNNT(9, 9) is larger than that between polynucleotides and BNNT(5, 5), which leads to the fact that dispersion of BNNT(9, 9) is better than that of BNNT(5, 5) with the assistance of polynucleotides in aqueous solution. Our study revealed the molecular-level dispersion mechanism of BNNT with the assistance of polynucleotides in aqueous solution. It shades a light on the understanding of dispersion of single wall nanotubes by biomolecules.