Abstract: Based on the data set of industrial structure heights at the county level of Xinjiang，this paper constructs the spatial Markov chains to analyze the spatio-temporal dynamics evolution of counties industrial structure. Firstly，the cosine method was used to calculate the industrial structure heights，which is proposed by China scholar Fu Linghui. According to the height values，the whole industrial structure heights were divided into four types: low level，medium-low level，medium-high level and high level. The industrial structure change trend was analyzed from time-space two dimensions；Secondly，according to the regional adjacency conditions the spatial weights were calculated and the space Markov matrix was built. In order to study surrounding environment influence，the evolution of regional industrial structures were analyzed. Finally，through the C-K equation the space transfer limit distribution matrix was set up for determining the county industrial structure height's long-term development direction and possibility. The results showed as follows：（1） County industrial structure of Xinjiang is increased from 2007 to 2011，but the number of low level and medium -low level is still more than 65% and there are only 8 high-level area.  On the whole，Xinjiang’s industrial structure is still in the lower stage. （2）Xinjiang’s industrial structure has regional differences，62 are in stable situation，20 in upward shift and 7 in downward shift. The pattern is as follows:  the middle being high and both sides being lower，and the north being high and the south being lower. From the limited distribution matrix，it was found that the probabilities of background areas of medium-high level and high level being changed into the low level's areas are 16.46% and 5.63%. It means that there is unstable problem in the upgrade of industrial structure of counties in Xinjiang. （3）the neighborhood effects of regional industrial structure evolution is weak on the northern slope of the Tianshan Mountains. In order to achieve the county industrial structure optimization and upgrading，this article sets up the following suggestion: To speed up the construction of key cities and backbone of transportation to form a “point - axis" situational development space；To accelerate opening to the west and developing the border areas；To quicken the construction of bonded area FTA and the development of port industry；To grasp the historical opportunity that the state supports Xinjiang construction；To enhance the ability of self-development．