The increasing phenomenon of non-grain production of cultivated land (NGPCL) in China poses a threat to food security and the rural ecological environment. The continued in situ urbanisation (ISU) of China’s counties has changed the pattern of arable land use and the structure of crop cultivation. However, to date, relatively few studies have focused on the impact of ISU on NGPCL, posing a challenge in rationally regulating NGPCL at different stages of urbanisation. Therefore, we investigated the ISU process and NGPCL in 781 counties within China’s Yangtze River Economic Belt (YREB) and analysed these dynamics using a segmented linear regression model. Our main finding is that both ISU and NGPCL levels have increased in the YREB during the study period, with the two showing a reversed trend in the east-west direction. In addition, ISU has a significant negative effect on NGPCL, particularly strong in the dimension of land urbanisation. This negative effect is mitigated as the quality of urbanisation improves over time. The results of this study provide insights into the internal mechanisms driving the evolution of the NGPCL at different stages of urbanisation in these districts and help find solutions to ensure food security and sustainable agricultural development.