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Lodging is the most important constraint for soybean growth at seedling stage in maize-soybean relay strip intercropping system. In the field experiments, three soybean cultivars Nandou 032-4 (shade susceptible cultivar; B1), Jiuyuehuang (moderately shade tolerant cultivar; B2), and Nandou 12 (shade tolerant cultivar; B3) were used to evaluate the relationship between stem stress and lignin metabolism in the stem of soybean. Results showed that the intercropped soybean was in variable light condition throughout the day time and co-growth stage with maize. The xylem area and cross section ratio played a main role to form the stem stress. The B3 both in intercropping and monocropping expressed a high stem stress with higher xylem area, lignin content, and activity of enzymes (phenylalanine ammonia-lyase (PAL), 4-coumarate: CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), peroxidase (POD)) than those of B1 and B2. Among the soybean cultivars and planting pattern, lignin content was positively correlated with stem stress. However, a negative correlation was found between lignin content and actual rate of lodging. In conclusion, the shade tolerant soybean cultivar had larger xylem area, higher lignin content and activities of CAD, 4CL, PAL, and POD than other soybean cultivars in intercropping. The lodging in maize-soybean intercropping can be minimized by planting shade tolerant and lodging resistant cultivar of soybean. The lignin content in stem could be a useful indicator for the evaluation of lodging resistance of soybean in intercropping and activities of enzymes were the key factors that influence the lignin biosynthesis.