Under the background of regional economic structure reform, the incomplete circulation of factor resources has aggravated regional asymmetry of monetary policy. This paper uses 2003-2015 year provincial panel data to analyze the effect of factor market segmentation on the regional output effect of China's monetary policy, and point out that the factor market segmentation has counteracted the effect of the output effect of monetary policy in China. The counteraction of the eastern and western regions found that: under the conditions of expansionary monetary policy, the scale and yield of capital goods in the eastern region are higher, the labor market is more active and the reconfiguration space is greater, and the division of factor market is more counterproductive to the effect of monetary policy.