Cadmium (Cd) contamination poses a serious threat to rice safety and productivity. This study investigated the potential of malic acid (MA), a key metabolic organic acid, to mitigate Cd toxicity and its genotype-dependent effects on cadmium uptake and essential element homeostasis in rice. Using hydroponic experiments with multiple genotypes, we found that MA application (0.5–1.5 mmol·L⁻¹) significantly reduced Cd accumulation in both roots and shoots, with the most effective reduction (up to 68.0%) achieved at 1.5 mmol·L⁻¹. Notably, genotype X24 was a low-Cd accumulator, while genotypes 20, 58, and 65 were high accumulators. Beyond Cd reduction, this study reveals the profound and genotype-specific modulation of nutrient homeostasis by MA, including consistent suppression of K and enhancement of Ca across genotypes, and highly divergent responses in Mg, Mn, Fe, and Zn accumulation. Furthermore, MA dramatically alleviated Cd-induced inhibition of root morphology, particularly in the high-Cd genotype 58, increasing root length and tip number by 42.8% and 57.8%, respectively. Our results provide novel insights into the genotype-dependent rebalancing of essential elements under MA amendment, highlighting the crucial role of genetic background in plant responses to organic acid treatments. These findings provide a mechanistic basis for developing MA-based foliar conditioners and genotype-specific strategies for managing Cd contamination in rice.