The main objectives were to evaluate the substantial equivalence of metabolite composition in transgenic rice and its parents， and assess the risk factors in rice from two aspects of metabolomic variation and mycotoxin content. High performance liquid chromatography-mass spectrometry (HPLC-MS) was used to analyze Japonica rice varieties Nipponbare (FP1) and PJ574(FP2) and their corresponding transgenic lines (FT16 and FT23). The results were as follows: multivariate statistical methods such as principal component analysis and partial least squares discriminant analysis were used to detect 448 metabolites from rice samples. Different metabolites were screened and it was found that the concentration variations of zearalenone， L-lactate， 10E， 12Z-octadecanodienoic acid and spermine were significantly affected by gene modification or variety differences. There were 9， 23 and 13 unique differential metabolites in group FP1-FP2， FP1-FT16 and FP2-FT23， respectively， with the highest variation in FP1-FT16. The unique differential metabolites of group FP1-FT16 mainly included deoxyguanolate， coffee salt and gluconic acid. The distinct metabolites of FP2-FT23 were mainly prostaglandin B2， L-cystine， 16-hydroxypalmitic acid. The unique differential metabolites of FP1-FP2 consisted of inositol and stearate amides. The effects of transgenic breeding and variety differences were similar， both of which affect arginine biosynthesis and multiple amino acid metabolic pathways to a certain extent， but the variation of metabolic pathways in different varieties of transgenic rice was different. Enzyme-linked immunoassay (ELISA) showed that the zearalenone content in rice samples ranged from 4.2 to 6 μg/kg， with a significant difference between the two parent varieties(P<0.01)， but the content of zearalenone in transgenic rices was substantial equivalence to that in the parents. Fusarium was found to be a common endophytic fungus in rice by high-throughput sequencing. Conclusions: Although the variation of metabolic components and metabolic pathways induced by transgenic breeding may affect the nutritional quality of rice， the extent of variation is not greater than that of rice varieties， and it is within the safe range. A low dose(less than 6 μg/kg) of Fusarium toxin zearalenone was detected in rice samples from four rice samples by untargeted metabolomic analysis technique. Although lower than the national standard (60 μg/kg)， Fusarium toxin may be synthesized by endophytic Fusarium fungi in rice， and there is a risk of fungal outbreaks under certain conditions with significant accumulation of toxicity.