Abstract: To improve the machining accuracy of the hole on the polystyrene microspheres for laser fusion, a fundamental understanding of the mechanisms of femtosecond laser ablation is required. We establish a molecular dynamics model of femtosecond laser ablation of polymers by optimally selecting the molecule representation model and related force field. Subsequent molecular dynamics simulations of femtosecond laser ablation of polyethylene and polystyrene show that the laser ablation-induced polymer material removal is caused by single chain ejection-accompanied surface evaporation and single chain motion-accompanied thermal expansion within the bulk. Furthermore, the microscopic deformation mechanisms of the single chain include inter-chain sliding and intra-chain change. It is found that the discrepancy in the molecule architecture has strong influence on the femtosecond laser ablation of polyethylene and polystyrene.