[Objective] The purpose of this paper is to reveal the spatial and temporal influence characteristics and mechanism of climate risk on the multi-functionality of farmland in the southwest border area, and to provide scientific basis for the sustainable use of land in the border area under the background of climate change. [Methods] Taking the southwest border region of China as the study area, this paper constructs a Climate Risk Index (CRI) encompassing drought, flood, high temperature, low-temperature freezing, and typhoon hazards. A three-dimensional evaluation framework of farmland multifunctionality—covering economic production, social livelihood, and ecological environment—is developed to analyze the spatiotemporal evolution of climate risk and farmland multi-functionality from 2008 to 2023. Furthermore, a panel vector autoregression (PVAR) model is employed to identify the dynamic effects and underlying mechanisms of climate risk on farmland multi-functionality. [Results] (1) Climate risk shows an overall trend of “steady increase followed by stabilization,” with a spatial pattern characterized by “high in the west and low in the east, strong in the south and weak in the north,” and partial improvements after 2018. (2) Farmland multifunctionality has improved overall, but its evolutionary rhythms differ markedly across dimensions: the economic function exhibits a “fluctuating increase,” the social function shows a “steady rise followed by deceleration,” and the ecological function demonstrates a “fluctuating increase with greater stability.” The composite function has gradually shifted from early “functional conflict” toward “coordinated development,” forming a dual-core pattern of “Baise–Chongzuo in Guangxi” and “Honghe–Xishuangbanna in Yunnan.” (3) Climate risk exerts significant short-term negative shocks on all functional dimensions, with the ecological function showing a “decline followed by stabilization.” Variance decomposition results indicate that by the 10th period, the contribution rates of climate risk to the economic, social, ecological, and comprehensive functions reach 5.46%、3.85%、3.80% and 5.28%, respectively. [Conclusion] Climate risk significantly undermines farmland multi-functionality in the southwest border region, particularly in the economic and social dimensions, while the ecological function demonstrates stronger resilience. The findings provide empirical evidence and scientific support for coordinating multi-functional farmland use and promoting sustainable regional development in border areas under climate change.