Malic acid (MA) plays an important role in plant tolerance to toxic metals, but its effect in restricting the transport of harmful metals remains unclear. In this study, japonica rice NPB and its fragile-culm mutant fc8 with low cellulose and thin cell wall were used to investigate the influence of MA on the accumulation of 4 toxic elements (Cd, Pb, Ni, and Cr) and 8 essential elements (K, Mg, Ca, Fe, Mn, Zn, Cu and Mo) in rice. The results showed that fc8 accumulated less toxic elements but more Ca and glutamate in grains and vegetative organs than NPB. After foliar application with MA at rice anthesis stage, the content of Cd, Pb, Ni significantly decreased by 27.9–41.0%, while those of Ca and glutamate significantly increased in both NPB and fc8. Therefore, the ratios between Cd and Ca in grains of NPB (3.4‰) and fc8 (1.5‰) were greatly higher than that in grains of NPB + MA (1.1‰) and fc8+MA (0.8‰) treatments. Meanwhile, the expression of OsCEAS4,7,8,9 for the cellulose synthesis in secondary cell walls were down-regulated and cellulose content in vegetative organs of NPB and fc8 decreased by 16.7–21.1%. However, MA application significantly up-regulated the expression of GLR genes (OsGLR3.1-3.5) and raised the activity of glutamic-oxalacetic transaminease for glutamate synthesis in NPB and fc8. These results indicate that hazard risks of toxic elements in foods can be efficiently reduced through regulating cellulose biosynthesis and GLR channels in plant by combining genetic modification in vivo and malic acid application in vitro.