Under the influence of global warming, flash drought events in China are gradually increasing, with the southwest region being particularly affected. The Chengdu-Chongqing area is experiencing increasing crop failures as a result of these flash droughts. However, understanding the resistance and recovery of farmland productivity to flash droughts is limited both domestically and internationally. Therefore, investigating the resistance and recovery mechanisms of farmland to flash droughts is of significant importance for protecting agricultural resources. The GPP data, Chinese soil moisture dataset, and farmland type data were used in the study. The fundamental characteristics of flash drought in the Chengdu-Chongqing area in 2006 and 2022 were investigated by using run length theory. Then, the study assessed the resistance and recovery capacities of farmland to flash droughts and quantified the vulnerability of farmland productivity in the Chengdu-Chongqing area. The main results reveal that the northwest and southeast parts of the Chengdu-Chongqing area experienced more severe flash droughts in the flash drought years of 2006 and 2022. Notably, areas such as De yang, Mian yang, and Chengdu exhibited high severity, and duration of flash droughts, while the number of flash droughts in the western region significantly decreased in 2022 compared to 2006. Compared to 2006, most farmland in 2022 has shown improved resilience but decreased resistance. Specifically, paddy fields, corn fields, and other single-season, double-season, and three-season crops have seen their resistance levels decrease from 5-6 to 3-4. Meanwhile, the range of resilience change has increased from 1-2 to 2-3. The range of resilience change has increased from 1-2 to 2-3, while the range of resistance change has decreased from 4-6 to 2-4. In 2022, the resistance time of farmland in the northern part of the Chengdu-Chongqing area increased compared to 2006, while the recovery time of most farmland in the Chengdu-Chongqing area sharply decreased. In 2022, farmland in the northwest of the Chengdu-Chongqing area became more vulnerable to flash droughts compared to 2006. During the flash drought year of 2022, multi-season crop fields in the Chengdu-Chongqing area exhibited higher vulnerability than single-season crop fields used in rotation. When facing flash droughts, the vulnerability of irrigated farmland was lower than that of rainfed farmland. However, the average vulnerability of some rainfed single-season farmlands, such as corn fields and wheat fields, was lower than that of irrigated farmland. This study enhances the understanding of farmland resistance and resilience to flash droughts and elucidates the impact mechanisms of flash droughts on farmland vulnerability under various irrigation and planting systems. It offers a scientific theoretical basis for agricultural production, drought resistance, and disaster reduction in the Chengdu-Chongqing area.