Soybean is an important legume food crop, and its seeds are rich in nutrients, providing humans and animals with edible oil and protein feed. However, soybean is sensitive to water requirements, and drought is an important factor limiting soybean yield and quality. This study used Heinong 84 (drought resistant variety) and Hefeng 46 (intermediate variety) as tested varieties planted in chernozem, albic, and black soils. The effects of drought stress on the activities of key enzymes in carbon metabolism and photosynthetic characteristics of soybean were studied during the flowering stage, most sensitive to water. (1) The activities of SS-1, 6PGDH, and G6PDH enzymes in soybean leaves first increased and then decreased under drought stress. The enzyme activity was the highest under moderate drought stress and weakest in the blank group. (2) Drought stress increased Phi2, PhiNO, and Fm in soybean leaves and reached the highest value under severe drought; with the increase in drought stress, PhiNPQ and Fv/Fm of soybean leaves gradually decreased, reaching the lowest under severe drought. (3) With the increase in drought stress, F0 and Fs of soybean leaves showed a single peak curve, and the maximum was at moderate drought. (4) Correlation analysis showed that F0 was greatly affected by varieties and soil types; Fs, F0, and Fm soil varieties had a great influence, and chlorophyll fluorescence parameters were affected differently under drought stress with different drought degrees. (5) Drought stress changed the agronomic traits and yield of soybean. With the increase of drought degree, plant height, node number of main stem, effective pod number, 100-seed weight and total yield decreased continuously. (6) Drought stress affected the dry matter accumulation of soybean. With the increase of drought degree, the dry matter accumulation gradually decreased. Among them, the leaf was most seriously affected by drought, and SD decreased by about 55% compared with CK. Under the condition of black soil, the dry matter accumulation of soybean was least affected by drought.