The effect of fertilizer supply and light intensity on the distribution of elemental contents (%C and %N) and light stable isotopes (C, N, H, and O) in different rice fractions (rice husk, brown rice, and polished rice) of two hybrid rice cultivars (maintainer lines You-1B and Zhong-9B) were investigated. Significant variations were observed forδ13C (−31.3 to −28.3‰),δ15N (2.4 to 2.7‰),δ2H (−125.7 to −84.7‰), andδ18O (15.1‰ to 23.7‰) values in different rice fractions among different cultivars. Fertilizer treatments showed a strong association with %N,δ15N,δ2H, andδ18O values while it did not impart any significant variation for the %C andδ13C values. Light intensity levels also showed a significant influence on the isotopic values of different rice fractions. Theδ13C values showed a positive correlation with irradiance. Theδ2H andδ15N values decreased with an increase in the irradiance. The light intensity levels did not show any significant change forδ18O values in rice fractions. Multivariate ANOVA showed a significant interaction effect of different factors (light intensity, fertilizer concentration, and rice variety) on the isotopic composition of rice fractions. It is concluded that all environmental and cultivation factors mentioned above significantly influenced the isotopic values and should be considered when addressing the authenticity and origin of rice. Furthermore, care should be taken when selecting rice fractions for traceability and authenticity studies since isotopic signatures vary considerably among different rice fractions.