Pruning treatment is one of the important management practices of perennial fruit tree cultivation. Combining fruit tree growth theory with mathematics model and software development is an effective way in agricultural research. Virtual apple tree is built as a case to study pruning treatment in this paper. First, architectural development of apple tree was analyzed and stored in xml file. Then, the simulation software of apple tree pruning is build based on the Qt framework and OpenGL graphics library. The interactive pruning and automatic pruning with setting conditions are realized in the software. Reaction laws of apple tree pruning are extracted from the analysis on the experiment data. Stochastic 3D apple tree architectures after being pruned also can be simulated. Result indicates that simulation is efficient, accurate and timely judgment of pruning reaction is possible. This work is the foundation of future research, which will simulate the apple tree development of architecture and biomass after pruning treatment over time.