Based on the patent application data and panel data of 367 prefecture-level city units in China from 2000 to 2024, this study measures the technological innovation capacity of China’s marine new materials industry, and analyzes the characteristics of its spatio-temporal evolution and the driving mechanism. The research shows that: The annual growth rate of the national innovation capacity level is 33.4%, presenting a "stepped" growth trend over time. The average annual value of the Gini coefficient is 0.851. The overall development shows a progressive trend, but there are significant differences in the internal scale. In terms of space, a distribution pattern with higher innovation capacity in the east and lower in the west along the coastline has been formed. The global Moran’s I index is significantly positive. Cities with a high level of innovation capacity are clustered in the Bohai Rim Economic Circle, the Yangtze River Delta Economic Circle, and the Pearl River Delta Economic Circle, indicating unbalanced development among regions. The driving mechanism of the spatio-temporal differentiation of innovation capacity has multi-dimensional interaction characteristics. In the economic and social aspects, high-tech enterprises drive the research, development, and transformation of innovative products. In the urban cultural aspect, the abundance of tourism resources promotes the reconstruction of the value of innovative technologies. In the ecological environment aspect, the trend of natural patches affects the willingness of innovative talents to reside. After cross-dimensional interactions, a significantly enhanced synergistic effect is generated.