To decrease d-lactic acid production cost, sugarcane molasses and soybean meal, low-cost agro-industrial wastes, were selected as feedstock. First, sugarcane molasses was used directly by Lactobacillus delbrueckii S-NL31, and the nutrients were released from soybean meal by protease hydrolysis. Subsequently, to ensure intensive substrate utilization and enhanced d-lactic acid production from sugarcane molasses and soybean meal, adaptation of L. delbrueckii S-NL31 to substrates was performed through adaptive laboratory evolution. After two-phase adaptive laboratory evolution, the evolved strain L. delbrueckii S-NL31-CM3-SBM with improved cell growth and d-lactic acid production on sugarcane molasses and soybean meal was obtained. To decipher the potential reasons for improved fermentation performance, a metabolomics-based approach was developed to profile the differences of intracellular metabolism between initial and evolved strain. The in-depth analysis elucidated how the key factors exerted influence on d-lactic acid biosynthesis. The results revealed that the enhancement of glycolysis pathway and cofactor supply was directly associated with increased lactic acid production, and the reinforcement of pentose phosphate pathway, amino acid metabolism, and oleic acid uptake improved cell survival and growth. These might be the main reasons for significantly improved d-lactic acid production by adaptive laboratory evolution. Finally, fed-batch simultaneous enzymatic hydrolysis of soybean meal and fermentation process by evolved strain resulted in d-lactic acid levels of 112.3 g/L, with an average production efficiency of 2.4 g/(L × h), a yield of 0.98 g/g sugar, and optical purity of 99.6%. The results show the applicability of d-lactic acid production in L. delbrueckii fed on agro-industrial wastes through adaptive laboratory evolution.