By constructing a new economic geography theory related to the premise of deduction, we deduce a new multivariate analysis framework of theory model, and get a inner relationship mechanism about technological progress, industrial agglomeration, urban scale and income gap between the urban and rural. Then, we build the technology progress, industrial agglomeration and urban scale empirical panel simultaneous equation model (SEM) and the least squares (OLS) regression empirical model of technological progress, industrial agglomeration, urban scale, and the income gap between urban and rural areas each other. And based on the Stata software of measurement, with the experience of China’s 23 large urban agglomerations data as sample, we respectively empirically test the whole of China urban agglomeration and the eastern, central and western four areas to compare the differences, and empirical test results are consistent with the results of the basic theory model. In terms of China’s urban agglomeration, we find that technological progress, industrial agglomeration and urban scale mutualy promote each other, and urban scale and industrial agglomeration will narrow the income gap between urban and rural areas, however, technological progress will expand the income gap between urban and rural areas.