Through a literature analysis, this study proposes that the difference between scientific innovation and technological innovation has been ignored in the current research on the level of scientific and technological innovation and its influencing factors. Combined with multidimensional proximity and knowledge type of current research, a theoretical induction has been carried on their corresponding relation with scientific innovation and technological innovation, research hypotheses were proposed the multidimensional proximity effect on the mode and degree of scientific innovation and technological innovation, five theoretical factors, which are the economic development level, regional economic structure, the level of opening to the outside world, science and technology input and education input, are proposed to affect the level of scientific innovation and technological innovation. In this study, the Yangtze River Delta region of China from 2001 to 2018 is selected as the research sample, and the two hypotheses proposed are tested through a mixed method of exploratory spatial data analysis and spatial panel econometric model. The main conclusions are as follows: i) As an exogenous variable, geographical proximity has a small impact on the level of scientific innovation, but a large impact on the level of technological innovation; ii) As endogenous variables, theoretical influencing factors may not play a significant role in the actual environment due to the complex influence of multidimensional proximity; iii) Based on the idea of improving multidimensional proximity and the actual situation of the region and the city, we can formulate policies conducive to improving the regional and urban innovation environment.