This study aims to capture the spatial and time influence of climate change on crop production efficiency (CPE) using the SE-SBM model combined with DEA window analysis. The model is validated with the data from 1976 to 2016 in Saskatchewan, one of the three Canadian prairie provinces. By categorising Saskatchewan into three regions: black soil zone, dark brown soil zone, and brown soil zone, differences are analysed between CPE without considering climate change and CPE under climate change. We find that CPE under climate change is significantly larger than CPE without consideration of climate change, and the positive influence of temperature fluctuations during the growth period on CPE is more important than that of humidity fluctuations, and the beneficial impact of average humidity on CPE is significantly greater than that of average temperature.