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How to reasonably evaluate the performance of scientific research activities in universities has attracted people's extensive attention. This study identifies the scientific research activity of Chinese universities as a two-process system with three sub-stages, including technical accumulation and research commercialization processes. Where, the process of technical accumulation includes the production of scientific research and patenting stage, while the process of research commercialization is a separate stage. First, this study proposes a network DEA model with two processes and three sub-stages to evaluate and decompose the performance of scientific research activities in universities. Secondly, taking 61 Chinese universities in the "Double First-Class" initiative (DFIU) as examples, this study evaluates the overall efficiency, stage efficiency and coordination efficiency of scientific research activities in Chinese universities. The final main conclusions are as follows: (1) The average score associated with the transformation efficiency of scientific research achievements based on the internal structures is only 0.2406, lower than the CCR efficiency and merger efficiency, indicating that most universities are still facing problems such as low resource utilization efficiency or unsatisfactory results. (2) The universities in the "First-class Discipline" construction plan (UFDCP) have outstanding performance in the technical accumulation process and the production of scientific research stage. Professional characteristics universities are generally much less efficient than polytechnic universities and comprehensive universities. (3) The universities in the "First-class Discipline" construction plan (UFDCP) are better than the universities in the "First-class Universities" construction plan (UFUCP) in terms of average efficiency values and polytechnic universities are better than other types of universities in terms of average efficiency values. We can find part of the reason for this difference in average efficiency from the evaluation of coordination efficiency. • This paper analyses the internal structure and internal operating mechanisms of research activities in universities. • Constructed a two-process network model with three sub-stages as a method to deal with unique efficiency decompositions. • The coordination efficiency of university scientific research system is calculated. [ABSTRACT FROM AUTHOR]