Polymer bonded explosive (PBX) belongs to energy materials, which generally consists of explosive crystals and binder molecules crystals. Thermal conductivity of PBX is a key parameter for evaluating its performance. Thus, its reliable and accurate calculation is a crucial scientific problem. However, the task becomes difficult because the accurate phonons dispersion relations calculated from first principles are almost unavailable. Therefore, lattice dynamics is proposed to accurately calculate phonon dispersion relations of molecular crystals (including TATB, HMX, PVDF, and PCTFE) in the present study. Then, Boltzmann theory is applied to calculate their thermal conductivities based on phonons of these molecular crystals. Our findings show that thermal conductivities are anisotropic along different crystal orientations. Finally, thermal conductivity of PBX has been calculated by two-flow network model. Our findings are in agreement with our and other researchers’ experimental results, thereby verifying that our lattice dynamics method is reliable in calculating phonons without imaginary frequency and the thermal conductivity of molecular crystals in PBX explosive can be calculated reliably. This condition solves the long-standing problem of inaccurate and unreliable thermal conductivity calculation. The study may be generalized to thermal conductivity calculation of any molecular crystal or any compound consisting of molecular crystals.