Abstract: In this study, we investigated the effects of an ecological rice-crab mode on the nutritional value of rice using two cropping patterns, ecological rice-crab (ERC) and rice monoculture (RM). Two japonica rice cultivars with good taste quality, 'Liaojing 433' and 'Wuyoudao No.4' (Daohuaxiang No.2), were selected as the study materials, and the rice contents of protein, amylose, and mineral elements, which are related to rice quality, were measured. Differences in the nutrition-related metabolites of ERC and RM were analyzed using non-targeted metabolomics. This study aimed to provide a theoretical basis for the application and popularization of the ecological rice-crab mode. The results showed that compared with RM, the protein content of brown rice of 'Liaojing 433' and 'Wuyoudao No.4' under the ERC mode significantly decreased by 6.75% and 10.11%, respectively, and Pb content decreased by 35.11% and 44.35%, respectively. The Fe content significantly increased by 1.03 and 3.99 times, respectively, and the Se content increased by 2.11 and 4.74 times, respectively. Two hundred and thirty-three metabolites were detected by gas chromatography-mass spectrometry (GC-MS). Significant differences in the metabolites were found between ERC and RM brown rice by partial least-squares discriminant analysis (PLS-DA). Compared with RM, the content of 4-aminobutyric acid in 'Liaojing 433' and 'Wuyoudao No.4' under the ERC mode increased significantly by 1.11 and 10.99 times, respectively; and the contents of antioxidant substances, such as alpha-tocopherol, beta-hydroxamic acid, and quinic acid, significantly increased by 0.62 and 1.22 times, 11.64 and 19.48 times, and 13.25 and 3.67 times, respectively. The hexitol content increased by 13.36 and 14.14 times, respectively, and the galactitol content increased by 2.13 and 1.87 times, respectively. Rice yield of 'Liaojing 433' under the ERC mode decreased by 286.0 kg·km^-2, whereas that of 'Wuyoudao No.4' under the ERC mode increased by 344.5 kg·km^-2. However, there were no significant differences in rice yield between ERC and RM. In conclusion, the ERC mode can increase the nutritional value of high-quality japonica rice without reducing its production.