Abstract: The effect of molybdenum and boron on photosynthetic efficiency of three soybean (Glycine max (L.) Merr.) varieties (Zhechun No.3, Zhechun No.2, 3811) with different treatment (without Mo and B, application of Mo alone, application B alone, application of Mo and B combination)were studied. The results showed that, soybean of application Mo and/or B exhibited an increasing of leaf area of photosynthesis, photosynthetic rates and respiration rate and a decrease of soluble carbohydrate of stem and leaf. The soybean of application Mo and/or B delaied decline of chlorophyll of soybean leaf and promoted soluble carbohydrate in the late stage of soybean. Among four treatments in our experiment, the effect of application Mo and B combination on photosynthetic efficiency of soybean was best. There was some difference between the physiological function of Mo and B. The effect of Mo on photosynthetic efficiency of soybean was greater than that of B on leaf area of photosynthesis, respiration rate and contents of chlorophyll of soybean leaf and the effect of B on photosynthetic efficiency of soybean is greater than that of Mo on photosynthetic rates, contents of soluble carbohydrate of pod or grain and partition ratio of dry matter. Some genetic variation of photosynthetic efficiency of three soybean varieties was found and had some variation in the responses to Mo and B among three soybean varieties.