The Rock Failure Process Analysis (RFPA2D) software developed by CRISR of Northeastern University, can well simulate the whole process of crack propagation in rock. This paper analyzes its data structure in depth, finds that the storage of its element is limited single structure, so its execution is slower. In order to overcome this flaw, this paper provides a simple method that can balance the memory's speed and disk's capacity by storing element's data with two different data structures.