Excessive rainfall provides a favorable condition for field mold infection of plants, which triggers field mold (FM) stress. If FM stress occurs during the late maturation stage of soybean seed, it negatively affects seed yield and quality. To investigate the responses of soybean seed against FM stress and identify the underlying biochemical pathways involved, a greenhouse was equipped with an artificial rain producing system to allow the induction of mold growth on soybean seed. The induced quality changes and stress responses were revealed on the levels of both transcriptome and metabolome. The results showed that soybean seeds produced under FM stress conditions had an abnormal and inferior appearance, and also contained less storage reserves, such as protein and polysaccharide. Transcriptional analysis demonstrated that genes involved in amino acid metabolism, glycolysis, tricarboxylic acid, β-oxidation of fatty acids, and isoflavone biosynthesis were induced by FM stress. These results were supported by a multiple metabolic analysis which exhibited increases in the concentrations of a variety of amino acids, sugars, organic acids, and isoflavones, as well as reductions of several fatty acids. Reprogramming of these metabolic pathways mobilized and consumed stored protein, sugar and fatty acid reserves in the soybean seed in order to meet the energy and substrate demand on the defense system, but led to deterioration of seed quality. In general, FM stress induced catabolism of storage reserves and diminished the quality of soybean seed in the field. This study provides a more profound insight into seed deterioration caused by FM stress.