The coordination of sustainable agricultural development is essential for optimizing agricultural policies and ensuring food security. However, only a few studies have examined the temporal and spatial aspects of the coordination of sustainable agricultural development systems in Northeast China. This study proposed a theoretical framework based on the dissipative structure theory, which suggests that the coordination among the four subsystems of economy, society, resources, and technology plays a crucial role in determining the level of sustainable agricultural development in Northeast China (SADINC). Then, the present study took socioeconomic statistical data as data sources and integrated administrative division data using the ArcGIS platform, forming spatial data for municipal-level units of SADINC from 2000 to 2020. The entropy weight method was applied to analyze the change in sustainable agricultural development, while the coordination degree model was used to analyze the coordination among different subsystems. The main results showed a general increase in the index of SADINC. The central part of the study area generally exhibits higher urban economic and resource indices, while the southern region exhibits higher urban social and technological indices. The average coordination degree of SADINC decreased from 1.736 to 1.639, representing a decline of 0.097. Moreover, the spatial polarization in most cities’ coordination degrees and subsystem indicators is not pronounced. However, there are characteristics of high-high agglomeration and low-low agglomeration. The high-high aggregation of the coordination degree shows a dispersal pattern from the large-scale agglomeration in the south-east to the central part. The distribution of low-low agglomeration transforms from large-scale agglomeration in the west to small-scale agglomeration in the northeast. The implementation of agricultural policies has dramatically impacted the increase in the index of each subsystem in Northeast China from 2000 to 2022. However, it is crucial to ensure coordination among the subsystems. Therefore, future policies should focus on strengthening the coordination among the economic, social, resource, and technology subsystems to achieve sustainable agricultural development.