The photo-thermal treatments in the current study were designed to simulate the natural conditions in three main soybean production regions in China, so the results could facilitate soybean breeding in those regions. The treatment of long day-length and spring-sowing in the current study is similar to the growth conditions in the northeast spring-sowing region, whereas the short day-length with spring-sowing and summer-sowing treatments resemble with the growth conditions in the south spring-sowing and south summer-sowing regions. The natural day-length with different sowing seasons in Beijing simulates the growth conditions of spring and summer-sowing soybeans in the Huang-Huai-Hai River Valley. The peak locus on Gm19 (Satt664) under the LD + LT treatment is a useful marker for marker-assisted selection of adaptation in the northeast China, whereas the loci Sat_135, Gm11_10847172, Gm11_33034954, and Gm20_3880320, could be utilized for selection in the Huang-Huai-Hai River Valley. The markers, Gm16_30766209 and Gm11_36124908, detected in both the LD and SD conditions could be utilized for selection in both northeast and south China.