The economies of large countries are different from those of small countries, and regional coordinated development is a prominent and important theoretical issue for large countries. The intra-regional and inter-regional misallocation of resources will be one of the most important factors that impede regional coordinated development, highlighting the importance of identifying the endogenous factors of resource misallocation. At present, the major part of the study on resource misallocation is conducted within the Hsieh & Klenow (2009) Framework and the General Equilibrium Framework, both of which attach great importance to the initial investment at the starting point of production and neglect the investment in the production process, which easily leads to the overestimation of resource mismatch. To approach the issue, this article focuses on the investment in the production process, and includes it in the production function together with the initial investment. Under the general condition of variable returns to scale, the article proposes a three-element resource mismatch accounting model which includes capital, labor force and process investment, and derives a specific approach to estimating the potential output capacity. On the basis of this theory, the article uses the microcosmic data of the database of Chinese industrial enterprises from 2001 to 2007 to estimate the resource mismatch and the potential production capacity of each region in China, and to study how the energy input affects the mismatch of regional resources. The following three findings are reached (1) Compared to the two-factor HK Framework, the three-factor accounting framework which includes the initial investment and the process investment can significantly reduce the overestimation of resource mismatch. (2) At the mismatch level, in the sample period, the mismatch situation of Chinese manufacturing industry has gradually improved. The problem of resource mismatch in China is most prominent in capital elements, and the importance order of factor resource mismatch is: capital> labor force> process investment, with the degree of mismatch of the latter two being very close. (3) In terms of the spatial pattern of resource mismatch, the capital mismatch is concentrated in the central and western provinces, and the labor mismatch is concentrated in the central and western provinces. The mismatch is mainly distributed in the provinces dominated by heavy chemical industry. (4)The process investment of energy sources have had a significant impact on regional resource mismatches, among which energy efficiency can reduce the mismatch of capital, labor, and process investment at the level of efficiency. However, at the quantitative level, the energy gap and energy loss exacerbates the mismatch between labor force and process investment, but does not have significant impact on capital mismatch. The proportion of heavy chemical industry will intensify the mismatch, and the impact of financial subsidies and foreign investment is uncertain. On the basis of theory and empirical studies, we put forward the following policy suggestions: First, gradually adjust China's energy-based energy structure, speed up energy efficiency, promote China's energy marketization process, and gradually straighten out benign alternative or complementary mechanisms of process investment and capital and labor. Second, promote the construction of a comprehensive modern energy transportation system, cut energy losses and reduce the distortion of industrial production factors. In addition to the basic energy transfer function, the comprehensive utilization of the energy transport system also has the function of optimizing the allocation of energy and environmental resources.