Since boron nitride nanotubes (BNNTs) were first manufactured, they have gained considerable attention for their wide-scale application as reinforcing composites, piezoelectric materials, electrical insulating materials, thermal conductors, and neutron shielding materials because of their excellent mechanical, electrical, thermal, and neutron absorption properties. Despite the remarkable properties and broad application scope of BNNTs, their use has been limited because of their ineffective structural control due to the presence of one-dimensional nanoparticles. To overcome this limitation, we investigated an approach for the collective self-assembly of BNNTs by using block copolymers (Pluronic P65 and Pluronic P85) as a template and studied the BNNT-induced phase behavior of the block copolymer. For homogenous mixtures of BNNTs and block copolymers, the BNNTs were encapsulated by the in situ polymerization of surfactants (p-BNNTs), where their overall structures were confirmed by small-angle neutron scattering (SANS) and atomic force microscopy (AFM) measurements. The p-BNNTs were mixed with the block copolymers (at 50%, Pluronic P65 or Pluronic P85) by centrifugation in alternative directions to form homogeneously mixed complexes. Polarized optical microscopy (POM) and small-angle X-ray scattering (SAXS) measurements confirmed a two-dimensional hexagonal structure of the BNNTs in the block copolymer matrix that self-assembled upon heating, which can give a possibility of being used as effective piezoelectric materials for energy harvesting. Moreover, upon the addition of BNNTs, the phase behavior of the block copolymer can be controlled, allowing the formation of hexagonal, face-centered cubic, and body-centered cubic structures depending on the BNNT concentration and temperature. This study provides a new and simple method to control the collective BNNT structure.