At present, the allocation efficiency of regional scientific and technological resources is low, and there are few research studies on social equity and economic efficiency. Therefore, this paper puts forward the allocation method of regional scientific and technological resources based on rationality. With the support of rationality perspective, the evaluation model of reform path of regional scientific and technological resource allocation is constructed to analyze the economic benefits and equity benefits of regional scientific and technological resource allocation. According to the principle of optimum allocation of regional science and technology resources, three-dimensional structure is constructed to maximize national investment and benefit and determine the optimal Pareto of resource allocation to measure the efficiency of resource allocation. The evaluation index system of the reform path of resource allocation is constructed by selecting the evaluation index of the reform path of resource allocation. The benchmark platform of big data was selected to generate data sets to be processed, and the spark on yam platform was used to submit jobs and generate spark job running data sets. The operation performance prediction model was established to optimize the configuration parameters of regional science and technology resources. The analysis results show that the designed method has high configuration capability and good effectiveness.