Tax system structure is one of the reasons affecting the regional economic growth difference. Regional economic growth effect is analyzed based on the measurement of the effective tax rate of labor income, capital income and consumption expenditure in the east, middle and west of China during 1995-2014. The research shows that the effective tax rate of labor income is overall low, that the effective tax rate of capital income is totally high, that the effective tax rate of consumption expenditure is stably rising, that the effective tax rate of labor income is lowest in the east but is highest in the west, which deviate from economic development level, and that the effective tax rate of capital income and consumption expenditure is high in the east and is low in the west, which are basically consistent with economic development level. The effect of economic growth of tax system structure change appears in current stage in each region and has obvious heterogeneity, labor income tax rate change is beneficial to the eastern region’s economic growth, and the tax rate change of capital income and consumption expenditure has boosting effect on the economic growth of each region but the effect size is different. We should sufficiently understand the regional discrepancy of the effect of tax system on economic growth and construct tax system and tax structure fitting for the economic development level in order to boost the coordinated development of regional economy.