Abstract: This paper analyzes the relationship between regional factor flow, industrial structure change and the regional economic divergence from two aspects of theoretical model analysis, and simulation based on Chinese actual data. The theoretical model of two regions and three sectors constructed in this paper reveals that the reason for the evolution of the regional economic divergence lies in the adjustment of regional industrial structure, while the root of the adjustment of regional industrial structure lies in the interdependence in the process of capital flowing and heterogeneous labor migration. The theoretical model and analysis process proposed in this paper can be used to explore the economic structure characteristics of any economy in any period. Applying this theory and method to China's practice, the simulation results show that the adjustment of industrial structure characterized by modern technology has resulted in the expansion of the economic divergence between regions in China, while the demand of production factors caused by different industrial structures leads to factor flowing continuously，and has further resulted in the imbalance of the development of industrial structure among regions, thus forming a positive feedback mechanism, which is referred as "factor chasing technology" Phenomenon. Besides, in the context of factor flowing, the coordinated development among industries is the key to determine the sustainable growth of the regional economy. The development of the high-tech industry needs the corresponding scale support of traditional service industry. At the same time, the development of the traditional service industry forms a feedback mechanism for the the high-tech industry. Therefore, only by strengthening the introduction of technological resources, making up for the technological differences between regions, and guiding the coordinated layout and development of industries and services between regions, it can effectively reduce the economic divergence between regions.