The iterative Multilevel Averaging Weight (MAW) algorithm presented in paper [1] is modified to solve the dynamic load imbalance problems arising from the two-dimensional short-range parallel molecular dynamics simulations in this paper. Firstly, five types of load balancing models are given which allows detailed studies of the algorithm. In particular, it shows that for strip decomposition, the number of iteration needs for the system to converge from an initially unbalanced state to a well balanced state is bounded by 2 log P , where P is the number of processors. This result can permit the algorithm to efficiently track fluctuations in the molecular density as the simulation progresses, and is much better than that of the Cellular Automaton Diffusion (CAD) scheme presented in paper [2] . Secondly, we apply MAW algorithm to solve the load imbalance problem in the parallel molecular dynamics simulation for higher speed wall collisions. At last, the numerical experimental results and parallel computing performance with MPI-1.2 under a PC-Cluster consists of 64 Pentium-III 500 MHz nodes connected by 100 Mbps Switches are given in this paper.