Climate change-induced variations in temperature, precipitation, and related factors substantially threaten crop yield, thereby jeopardizing food security. In the context of the Kangsabati river basin in India, where rice cultivation is vital for farmers’ livelihoods and food security, understanding the potential impacts of climate change on rice production becomes imperative. The interconnection of water, energy, and food (WEF Nexus) underscores the need to explore how alterations in food security, driven by climate change-induced crop yield changes, may reverberate across water and energy security. This study addresses a notable gap by utilizing the CMIP6-GCM to estimate climate change effects on crop yield, explicitly focusing on the Kangsabati River basin. Unlike previous research, this investigation integrates the influence of climate change-induced crop yield on the WEF Nexus at the basin level. The AquaCrop model is employed to simulate rice yields across historical (1981–2014), near-future (2021–2060), and far-future (2061–2100) periods under two climate scenarios (SSP245 and SSP585) using the EC-Earth3 GCM model. Findings indicate a projected decline in crop yield for both seasons (Kharif and Rabi) in both SSP245 and SSP585 scenarios. SSP245 anticipates a 10–15% decrease in Kharif paddy yield and a 15–20% reduction in Rabi season, while SSP585 predicts a more severe decline of 15–20% in Kharif and 20–25% in Rabi. Furthermore, the study reveals a diminishing trend in the Food Sub-index (FSI) and Water-Energy-Food Nexus Index (WEFNI), with SSP585 exhibiting a more pronounced decrease than SSP245. Notably, downstream areas in the basin demonstrate higher food and overall WEF security than other regions. These insights are instrumental for policymaking, enabling the formulation and implementation of sustainable water, energy, and food security strategies that account for the anticipated impacts of climate change in the Kangsabati River basin.