Abstract: With the acceleration of industrialization, urbanization and modernization, the binding force of urban resources and environment is continuously increasing, and the ecological security of urban agriculture is worth paying attention to. Based on the PSR model, this paper constructs the evaluation index system of urban agriculture ecological security in Pearl River Delta, and comprehensive evaluation for urban agriculture ecological security in Pearl River Delta and analysis of related obstacle factors has been carried out by applying the comprehensive index method, the entropy value method and obstacle degree model. The results showed that: from 2006 to 2015, the comprehensive index of urban agriculture ecological security in Pearl River Delta has been gradually improved. The urban agriculture ecological pressure of Shenzhen and Zhongshan is larger, the urban agriculture ecological status of Dongguan is relatively poor, and the urban agriculture ecological response of Zhaoqing and Jiangmen is relatively weak. The indexes of urbanization rate, cultivated land per capita etc. became major obstacle factors to the ecological security of urban agriculture. The Pearl River Delta region should vigorously strengthen the protection of cultivated land resources, continue to promote the urban ecological environment and agricultural non-point source pollution control, so as to ensure the stable development of urban agriculture ecological security.