The allocation efficiency of Chinese incubation has been widely concerned, but there is little research study from a process dimension and find the regulation in the business growth. This paper uses a two-phase (technical innovation and technology transformation) network DEA method to study the technological innovation and technological transformation efficiency of Chinese provinces. The Malmquist production index was also used to analyze the dynamic changes in efficiency. The results show that, first, relative to the efficiency of science and technology innovation in the first phase, the efficiency of the second phase of science and technology transformation has a greater impact on the efficiency of resource allocation. Second, there are obvious regional differences in the efficiency of domestic incubator resource allocation. Third, through analysis of the Malmquist Index, it is found that technological progress has a greater effect on productivity than technical efficiency, both for the overall and the innovation and transformation stages. At the same time, resource allocation efficiency will be affected by macroeconomic conditions. The research have important reference value for the improvement of the resource allocation and the formulation of relevant policies.