<p>The impact of variations in soil properties in agricultural lands on rice grain quality, mainly elemental composition, is a critical issue for human health. Among all the chemical properties of soil, organic matter plays a vital role in enhancing soil fertility and quality as a sustainable strategy. The uptake of minerals and toxic heavy metals in rice plants mainly depends on the degradation rate of organic matter in the soil. However, the relationship between the organic matter in soil and the concentrations of both essential and toxic elements in rice grains has been poorly addressed. Therefore, the present study was conducted to investigate the impact of organic matter in soil on the elemental composition of rice grains for three consecutive years in the rice cropping system with cultivation seasonal variation. Overall, Pearson correlation analysis showed that the organic matter content in soil was positively correlated with the concentrations of B, Mg, Al, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Sb, Ba, Pb, and P in rice grains. Among these elements, significantly positive correlations (<i>P</i> &lt; 0.01) were observed between organic matter in soil and Mg, Ca, Cr, Co, Ni, and Cu in rice grains. Furthermore, the strongest and most consistent element-to-element correlations were observed among Mg, K, Ca, Cr, Al, Fe, Mn, Co, Ni, Cu, and Cd in rice grains. This study also highlights the beneficial influences of various environmental factors on the decomposition of organic matter in soil which leads to creating alterations of the profile of minerals and toxic heavy metals in rice grains even in the same locations with time. In addition, this study revealed that improving the grain quality and minimizing the environmental pollution by toxic heavy metals can be endeavored by adding organic amendments instead of applying chemical fertilizers to enrich the paddy soil.</p>