As China has entered a new stage of high-quality development, clarifying the mechanism and spatial characteristics of green development for urban agglomerations are critical to sustainable development. Based on the data of 11 major cities in the Harbin-Changchun urban agglomeration (HCUA) from 2010 to 2020, this study constructs an evaluation system of green development index (GDI) is composed of four dimensions, i.e. urban green construction (UGC), industrial green development (IGD), resource and environmental carrying capacity (RECC), and technological innovation support (TIS). Furthermore, using the entropy weight method to obtain the weights of evaluation indicators. And then, the comprehensive index calculation is used to evaluate the GDI. The driving factors of each level of GDI are determined by the Pearson correlation coefficient. The results infer some novel findings as follows: (1) the overall tendency of the GDI of the HCUA has gradually increased from 0.358 in 2010 to 0.379 in 2020 which is at the average level. The dimension of TIS shows the highest rate of contribution while IGD and RECC show a fluctuating trend over the time window. (2) The GDI in the HCUA exhibits a patchy clustering differentiation feature that spreads from the central area to the surrounding areas with a “high in the south and low in the north” pattern. Specifically, Changchun, Harbin, and Daqing form an “inverted triangle” structure in geographical location to drive the green development of neighboring areas. (3) The core cities of the HCUA, Changchun, and Harbin, show a much higher level than the other cities. Jilin and Daqing are at the average level, and besides, the rest of the cities of GDI are at the poor level with significant fluctuations in ranking. (4) There are different driving factors between each level of GDI. For cities with good and average levels should focus on protecting resources and the environment. Meanwhile, cities with poor level of GDI need to improve IGD to optimize the urban green structure. Thus, it is suggested to strengthen the flow of factors and implement differentiated strategies to promote coordinated development and spatial clustering.