To investigate the high-quality and efficient development of the manufacturing industry in the Central Plains Urban Agglomeration (CPUA), this paper uses the three-stage Data Envelopment Analysis (DEA) and Malmquist index model to evaluate and analyze the manufacturing development efficiency of 30 prefecture-level cities in five provinces of China in the CPUA from 2017 to 2022. First, the DEA model is applied to evaluate the comprehensive efficiency of the manufacturing industry in 30 regions of the CPUA; second, the Stochastic Frontier Analysis (SFA) regression model is used in conjunction with the technical efficiency and scale efficiency of the manufacturing industry to deeply explore and adjust the causes of the current situation in various regions; finally, after re-analyzing the efficiency with the corrected input-output data, the Malmquist index model is used to analyze the total factor productivity index and its decomposed efficiency of the manufacturing industry in the CPUA from 2017 to 2022. The study shows that the pure technical efficiency (PTE) of the 30 prefecture-level cities in the CPUA from 2017 to 2022 is stable and relatively good, and the main reason for the overall low comprehensive efficiency is the poor scale efficiency; after excluding the interference of environmental factors, the average comprehensive efficiency of each city is lower than before the adjustment, with environmental factors and random errors having a significant impact on the manufacturing industry, especially in Bengbu City; the main factor in the decline of the total factor productivity of the manufacturing industry in the CPUA is the hindrance of technological progress; the spatial distribution of the comprehensive efficiency of the manufacturing industry in the CPUA generally shows a pattern of "higher efficiency in the middle, lower efficiency at the edges", and there is a situation of regional development imbalance in the high-quality development level of the manufacturing industry in the 30 regions.