To clarify the yield benefits of biochar application in maize and soybean intercropping and its effects on rhizosphere microbial functions, a two-year field experiment was conducted in Putian, Fujian Province, China, from 2025 to 2026. The experiment included three cropping systems, namely maize monocropping (MM), soybean monocropping (MS), and maize and soybean intercropping (SM), combined with two fertilization regimes: conventional chemical fertilization (CF) and biochar combined with chemical fertilizer (BF). We evaluated crop yield, rhizosphere soil physicochemical properties, enzyme activities, and microbial carbon-source utilization. The land equivalent ratio (LER) of maize and soybean intercropping remained above 1 in both years, indicating a stable land-use advantage. Compared with the corresponding monocropping treatments under conventional fertilization (MM-CF and MS-CF), SM-BF significantly increased maize and soybean yields by 29.40% and 34.78%, respectively. In the maize rhizosphere, SM-BF increased polyphenol oxidase, peroxidase, urease, and sucrase activities by 29.63%, 17.89%, 17.98%, and 35.03%, respectively, whereas the corresponding increases in the soybean rhizosphere were 27.96%, 17.89%, 26.10%, and 35.03%. These enzyme activities were the highest among all treatments. SM-BF also maintained relatively high levels of available N and available P in the maize rhizosphere and total N, available N, available P, and available K in the soybean rhizosphere. Biolog analysis showed that SM-BF generally resulted in the highest average well color development (AWCD) and microbial utilization of amino acids, polymers, carboxylic acids, and carbohydrates. Principal component analysis further showed that the cropping system contributed substantially to variation in rhizosphere microbial carbon-source utilization, while fertilization also had a detectable effect. Overall, maize and soybean intercropping showed a stable land-use advantage. Under biochar combined with reduced chemical fertilizer, the intercropping system maintained relatively high rhizosphere nutrient levels, enzyme activities, and microbial carbon-source utilization. These results suggest that interspecific interactions and fertilization management may jointly regulate the rhizosphere environment and microbial functional characteristics, which may be associated with the yield advantage of intercropping. This study provides a theoretical basis for efficient nutrient management and reduced chemical fertilizer input in maize and soybean intercropping systems.