Chilling stress affects growth and yield of warm-climate crops such as soybean (Glycine max L.) that is susceptible to low temperature (10-18℃). A comparative proteomic approach was employed to explore the mechanisms underlying soybean response to chilling stress. Soybean seedlings were germinated for 3-4 days and exposed to low temperature (10℃) for 3 days, and the proteins were extracted from seedling leaves. Protein separation by SDS-PAGE followed by liquid chromatography electro-spray ionization tandem mass spectrometry (LC-ESI MS/MS) was effective approach to identify proteins, based on the number of peptides reliably identified. A total of 77 proteins out of 704 proteins were identified in the presence of chilling stress. Most proteins identified had functions related to cell signaling, metabolism, energy and transport, protein biosynthesis and degradation, cytoskeleton, and were involved in regulating reactions and defending against stress. It is therefore likely that the response of soybean plant’s proteome to chilling stress is complex, and that the identification proteins may play an important role in regulating adaptation activities following challenge to chilling stress to facilitate cellular homeostasis. Furthermore, our result suggest that new ways of engineering stress-tolerant plants responding climate change by providing outline for agriculturally important chilling stress.