Laser crystallization of amorphous Si thin films is one of reliable method of preparing nanocrystalline silicon with high density and controllable size. In the present work, molecular dynamics simulation based on Tersoff potential was used to study the laser crystallization process of ultrathin amorphous silicon film (2.7 nm) on amorphous silicon nitride substrate. The influence of laser fluences on the crystallization and formation of nanocrystalline Si was investigated. It was found that there exists a laser fluence window in which nucleation and growth of nanocrystalline Si can be realized, which is in agreement with our previous experimental observations. The nucleation and growth processes in microscopic scale were simulated and the size of formed nanocrystalline Si was limited in both vertical and lateral directions by the film thickness and the formation of grain boundaries.