Intercropping is a sustainable agricultural practice used worldwide for highly efficient utilization of resources. However, short crops often grow under the shade of the canopy of tall crops in intercropping systems. Plants evolved two main strategies to deal with shade: avoidance and tolerance. Soybean (Glycine max), a legume crop, is often planted in intercropping. But little is known about a strategy that soybean may employ to deal with shade at seedling stage. Therefore, we determined morphological and physiological traits related to shade tolerance and shade avoidance in seedlings of two varieties. Generally, both varieties showed similar shade tolerance traits, such as increased specific leaf area and chlorophyll (Chl) content, and reduced photosynthetic capacity and the Chl a/b ratio. The light-limiting environment eliminated the benefits of shade tolerance traits for the carbon gain, which led to similar real-time photosynthesis and biomass in intercropping. By contrast, two varieties expressed different changes in shade avoidance traits. The variety Guixia 3 exhibited clear preference of shade avoidance that resulted in a high main stem, hypocotyl elongation, and biomass allocation towards the stem. The variety Gongxuan 1 showed those traits less. We suggested that the genetic variation occurs within soybean, thus the shade avoidance related traits might be important for variety selection for intercropping. Hence, the evaluation of performance should focus on shade avoidance in soybean genotypes in future experiments.