In maize-soybean intercropping system, soybean was shaded by the taller crop maize, and consequently, soybean seeds were under shade stress conditions during whole developmental stages. Subsequently, whether and how the shade stress influence the abiotic stresses tolerance of soybean seeds during germination? It is worthy of further study. In this study, soybean cultivar “Hedou19” and maize cultivar “Jundan26” were employed as the experimental materials. The maize-soybean intercropping (IC) system was two rows of maize and soybean crossed planting (1:1), and the soybean monocropping (MC) was as control. After soybean was harvested, the quality traits including 100-seed weight, protein content and fat content were measured and the ability of resisting adversity (high temperature, mannitol, glucose, PEG, NaCl and abscisic acid) during germination was analyzed. Finally, the expression of genes related to signal transduction of ABA was further analyzed by qRT-PCR assay. Results showed that there was no significant difference in 100-seed weight, fat content and protein content between monocropping and intercropping soybean seeds. Further, intercropping soybean seeds germinated faster than monocropping soybean seeds under abiotic stresses conditions (high temperature, mannitol, glucose, PEG, NaCl and ABA) and showed strong resistance to abiotic stresses. Further qRT-PCR demonstrated that the transcription levels of GmABI4 and GmABI5, positive regulators in abscisic acid (ABA) signaling pathway, in the intercropping soybean seeds were lower than that in monocropping soybean seeds. Therefore soybean quality did not change in maize-soybean intercropping system, it could enhances the abiotic stresses tolerance during germination processes, maybe primarily through weaken ABA signaling strengthen.