Herein, in order to design the formulation of fluoropolymer bonded explosives, common fluoropolymers were selected and added to the high energy density compound hexanitrohexaazaisowurtzitane (epsilon-CL-20). Molecular dynamics simulations were carried out on fluoropolymers (F2603, F2311, F2314, F2426, and PTFE) and fluoropolymers bonded epsilon-CL-20. Glass transition temperature (Tg) of fluoropolymers were calculated. Besides, the mechanical properties and physical compatibilities of epsilon-CL-20 based polymer bonded explosives were predicted. The calculated results show that the order of Tg of fluoropolymers is: PTFE>F2314>F2311>F2462 approximate to F2603 and Tg of F2603 increases as the degree of polymerization increases. The binding energy for fluoropolymers with epsilon-CL-20 is in the following order: epsilon-CL-20/F2462>epsilon-CL-20/F2603>epsilon-CL-20/F2314>epsilon-CL-20/F2311. All fluoropolymers interact with epsilon-CL-20 mainly in vdW force. The order of tensile modulues is: epsilon-CL-20>epsilon-CL-20/F2314>epsilon-CL-20/F2311>epsilon-CL-20/F2462>epsilon-CL-20/F2603, the orders of Poisson's ration () and the quotient bulk modulus (K)/shear modulus (G) are opposite.