The genetic diversity of phenolic content (PC), individual phenolic acids, vitamin E isomers (VE) and fatty acids (FA) in the whole grain rice were investigated. The most abundant phenolic acid was ferulic acid ranging from 155.6 to 271.1 μg/g and comprising approximately 40–57% of total phenolic acid (TPA). The predominant tocopherols (T) and tocotrienols (T3) were α-T (6.43–12.67 μg/g) and γ-T3 (12.88–32.75 μg/g). The unsaturated fractions of FAs accounted for 74–81% of the total FAs in rice. Most of the phytochemicals among phenolics and VEs showed significant differences between white and red rice, with red rice demonstrating significantly higher levels. However, white rice had higher content of oleic, linolenic, eicosenoic and total fatty acids than red rice. The wide genetic diversity in whole grain rice allows food processors to have a good selection for producing rice products, and breeders to have new rice lines that can be bred for high nutrient levels.