Flood frequency in river source regions is significantly affected by rainfall and snowmelt as part of climatic changes. A traditional univariate flood frequency analysis cannot reflect the complexity of floods, and when used in isolation, it can only underestimate flood risk. For effective flood prevention and mitigation, it is essential to consider the combined effects of precipitation and snowmelt. Copula functions can effectively quantify the joint distribution relationship between floods and their associated variables without restrictions on their distribution characteristics. This study uses copula functions to consider a multivariate probability distribution model of flood peak flow (Q) with cumulative snowmelt (CSm) and cumulative precipitation (CPr) for the Hutubi River basin located in northern Xinjiang, China. The joint frequencies of rainfall and snowmelt floods are predicted using copula models based on the Coupled Model Intercomparison Project Phase 6 data. The results show that Q has a significant positive correlation with 24-d CSm (r = 0.559, p = 0.002) and 23-d CPr (r = 0.965, p < 0.05). Flood frequency will increase in the future, and mid- (2050–2074) and long-term (2075–2099) floods will be more severe than those in the near-term (2025–2049). The probability of flood occurrence is higher under the SSP2-4.5 and SSP1-2.6 scenarios than under SSP5-8.5. Precipitation during the historical period (1990–2014) led to extreme floods, and increasing future precipitation trends are found to be insignificant. Snowmelt increases with rising temperatures and occurs earlier than estimated, leading to an earlier flood period in the basin and more frequent snowmelt floods. The Q under the joint return period is larger than that during the same univariate return period. This difference indicates that neglecting the interaction between precipitation and snowmelt for floods leads to an underestimation of the flood risk (with underestimations ranging from 0.3% to 22%). The underestimations decrease with an increase in the return period. The joint risks of rainfall or snowmelt according to various flood periods should be considered for rivers with multi-source runoff recharge in flood control design. This study reveals the joint impact of precipitation and snowmelt on extreme floods under climate change in river source regions. This study also provides a scientific basis for regional flood prevention and mitigation strategies, as well as for the rational allocation of water resources.