The essence of economic growth lies in the continuous changes in the structure of resource factors. China's economic development has entered into a new norm, whereby "supply-side structural reform" highlights the importance of factor structure in economic growth, and whereby the theory of "new structural economics" advocates that economic structure is determined by factor endowment structure. By expanding the MRW model of human capital, this paper constructed a new endogenous economic growth model which includes education investment, health investment, and industrial structure, and then exploratorily conducted an empirical study on the relationship between the element structure and economic growth in Chengdu-Chongqing Urban Agglomeration. The results showed that the industrial structure and the education investment of the human capital had a significant impact on the economic growth of Chengdu-Chongqing Urban Agglomeration, whereas the material capital, due to its excessive accumulation of stock, presented diminishing marginal returns and thus demonstrated a relatively weaker impact on economic growth. Meanwhile, the health investment of the human capital structure had a negative effect on economic growth due to the small increase in the mortality rate of the total population. Therefore, it is suggested that, in the process of economic growth, Chengdu-Chongqing Urban Agglomeration should improve the quality of investment in the human capital structure, to facilitate its optimal match ratio with the stock of material capital and the structure of industries, and ultimately to effectively coordinate all factor resources for a better and sustained economic growth in the region.