Unbalanced and insufficient development is a prominent problem in China’s period of economic transformation, and an accurate grasp of the current situation and evolutionary trend of innovation and economic development is of great significance in finding a solution and promoting regional coordinated development. This paper introduces the framework of functional data analysis to the study of both innovation and economic development in China, examining its spatial dynamic distribution and convergence characteristic in greater depth. Empirical results revealed the following. (1) Significant regional differences exist in the absolute level of China’s innovation development, with a balanced improvement in the development speed and growth potential. Significant differences exist in the absolute level and speed of economic development, but not in the potential energy of development as reflected by acceleration. (2) The σ(t) function of nationwide and regional innovation development shows a downward trend. There is σ(t) convergence in economic development nationwide and in the northeastern, eastern, and western regions, but the regional disparities in economic development within the six central provinces have not yet been effectively mitigated. (3) Nationwide and regional innovation development are in a state of β(t) convergence. There is significant β(t) convergence in the nationwide economic development, with a transition point from divergence to convergence in the northeastern, eastern, and western regions. However, the β(t) function of economic development in the central region shows a region-wide divergence. The findings of this paper have important policy implications for recognizing the balance and disparities in innovation and economic development among regions in China and promoting coordinated regional development.

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