Urbanization has been recognized as an effective measure to promote socioeconomic development; however, it leads to cropland and habitat loss and aggravates ecosystem services (ESs), which have not been sufficiently and systematically revealed from the perspective of agriculture–ecology–economy nexus (AEEN). To address these knowledge gaps, this novel study adopted a hotspot of urbanization to examine the response dynamics of ESs and agricultural production to urbanization, as well as their regime shifts and interactions, by employing statistical records, satellite images, and incorporating biophysical model-based ESs into AEEN. In the past four decades, Guangdong has undergone rapid urbanization and associated landscape transformations, represented by cropland and wetland shrinkage and urban expansion, particularly around central city clusters, which have caused ESs degradation and grain productivity reduction. According to the regime shifts of the AEEN sectors and their systematic responses to socioeconomic developments and policy interventions, nexus sector interactions between agriculture and the economy in Phase I (1980–1997) and Phase III (2009–2020) had positive effects, while those in Phase II (1998–2008) were negative because of cropland loss and industrial structure adjustments. Network structure analysis and spatial panel model further revealed that natural environmental, socioeconomic, and landscape composition and structural factors were determinants of ES evolution and regime shifts in AEEN. Structural change analysis and systematic perspectives are essential for understanding the consequences and determinants of urbanization on agricultural production and ecosystem state by placing ESs within AEEN, which is expected to support landscape management and policy formulations for coordinated development that balance multi-sector benefits.