Maize (Zea mays L.) in the North China Plain are often subject to continuous overcast rain, which causing waterlogging and shading simultaneously at flowering stage, leading to huge yield losses. The mechanisms of maize response to combined waterlogging and shading remain largely unknown. Here, yield losses mechanism underline single and combined waterlogging and shading at flowering stage was investigated by performing phenotypic, physiological and quasi-targeted metabolomics analysis. Compare to single stress, combined stressed plants showed lower photosynthesis, root absorption ability, and increased ovary abortion. Phenotype analysis of the reproductive tissues showed that the ovary abortion was immediate caused by the decreased emerged silk number. The results of carbon metabolism indicated that the changes in carbohydrate contents and sugar metabolic enzyme activities could not explain the ovary abortion. In addition, metabolomics analysis identified 25 specific metabolites increased in ovaries and eleven specific metabolites decreased in silks has a strong correlation with ovary abortion. These differentially accumulated metabolites are mainly amino acids and flavonoids, indicating the amino acids and flavonoids metabolites play an important role during the ovary abortion. These findings will lay the foundation for breeding stress-tolerant maize cultivars.