The study on the spatial pattern of the relationship between urbanization and economic development has a more clearly practical significance for the choice of regional urbanization and economic development path. However, the existing research on the relationship between China’s urbanization and economic development (RCUED) lacks the fine depiction of the prefecture-level units. Using 2000 and 2010 census data and the statistical analysis method, we uncovered the evolution characteristics of China’s urbanization and economic development and conducted a quantitative identification for the RCUED with improved methods using the quadrant map approach. In addition, we investigated the spatial correlation effect of the RCUED using the spatial autocorrelation analysis method. The results were as follows: 1) In general, a high degree of matching exists between China’s urbanization and economic development at prefecture-level units at the significance level of 0.01. The correlation coefficients between China’s urbanization and economic development in 2000 and 2010 were 0.684 and 0.741, respectively. 2) A significant regional difference exists in the RCUED at prefecture-level units. Based on a comparative analysis of 341 prefecture-level units in China in the two years, we found that prefecture-level units can be categorized as under-urbanization, basic coordination and over-urbanization in various areas. The distribution of the relationship between the urbanization and the economic development within provinces was similar, that is, most of the provincial capital cities were ahead of urbanization. 3) The distribution of the RCUED presents a significant spatial correlation and agglomeration effect. Over time, the spatial dependency of the RCUED has weakened and the spatial heterogeneity has increased. Northeast China has always been an area characterized by over-urbanization. The number of prefecture-level units classified as under-urbanization has begun to decline in Yangtze River Delta, and that of the Qinghai-Tibet Plateau has gradually increased.Meanwhile, prefecture-level units rich in resources have transformed from over-urbanization into under-urbanization along the northern border. There is a certain degree of path dependence effect in the change of typological areas of the RCUED. Units with “ Under-urbanization-under-urbanization” and units with “over-urbanization-over-urbanization” account for 73% of the total number of prefecture-level units in China, and they have evident spatial differentiation characteristics.