Many factors, such as soil, climate, and water source in the planting area, can affect rice taste and quality. Adulterated rice is common in the market, which seriously damages the production and sales of high-quality rice. Traceability analysis of rice has become one of the important research fields of food safety management. In this study, LC–MS-based non-targeted metabolomics technology was used to trace four rice samples from Heilongjiang and Jiangsu Provinces, namely, Daohuaxiang (DH), Huaidao No. 5 (HD), Songjing (SJ), and Changlixiang (CL). Results showed that the discrimination accuracy of the partial least squares discriminant analysis (PLS-DA) model was as high as 100% with satisfactory prediction ability. A total of 328 differential metabolites were screened, indicating significant differences in rice metabolites from different origins. Pathway enrichment analysis was carried out on the four rice samples based on the KEGG database to determine the three metabolic pathways with the highest enrichment degree. The main biochemical metabolic pathways and signal transduction pathways involved in differential metabolites in rice were obtained. This study provides theoretical support for the geographical origins of rice and elucidates the change mechanism of rice metabolic pathways, which can shed light on improving rice quality control.