Boron nitride films were synthesized with $N_2$ion flux of low energy, up to 100 eV, at different substrate temperatures of no heating, 200, 400, 500, and $800^{circ}C$, respectively. Boron was supplied by e-beam evaporation at the rate of $1.5AA$/sec. For all the conditions, hexagonal BN (h-BN) phase was mainly synthesized and high resolution transmission electron microscopy (HRTEM) showed that (002) planes of h-BN phase were aligned vertical to the Si substrate. The maximum alignment occurred around $400^{circ}C$. In addition to major h-BN phase, transmission electron diffraction (TED) rings identified the formation of cubic BN (c-BN) phase. But HRTEM showed no distinct and continuous c-BN layer. These results suggest that c-BN phase may form in a scattered form even when h-BN phase is mainly synthesized under small momentum transfer by bombarding ions, which are not reconciled with the macro compressive stress model for the c-BN formation.