In this paper，an agent-based computer simulation model was used to analyze the dynamic relationship between economic growth and income difference in a transition economy and to evaluate the empirical effects of negative income tax system. Micro agents in the economy interact with each other，form the economic networks and enable the economy to evolve forward through the intelligential evolutionary system. Based on the logical rules of the transition economy，the model finally gave the results of the simulation：when the economy finishes rapid transition and enters into stable development，by implementing negative income tax system，government can effectively decrease income difference while at the same time maintain rapid economic growth.