Abstract: Rice is a vital staple crop in China. The edible part of rice is the endosperm, and the content and distribution of nutrients and toxic elements in the different parts of the grain are key factors in determining the nutritional and hygienic quality of rice. To fully analyze the impact factors, such as the environment and variety, 18 rice varieties in the main and ratoon seasons from three ecological zones were used as test materials. By measuring the content, distribution, accumulation, and transport coefficients of 14 elements in different grain parts across the main and ratoon seasons, the common and differential rules of element accumulation and distribution in the main and ratoon seasons were summarized and clarified. The 14 elements were grouped into two categories. The first included, Mg, Zn, As, Cu, Se, and Cd, which were most concentrated in the bran. Mg, Cu, and As accounted for 10.1% to 45.7% in the barn, Zn and Cd ranged from 50.3% to 78.9% in the endosperm. The second included Si, Fe, Mn, Ca, Cr, Ni, Pb, and Co, which had the highest content in the husk and showed a layer-by-layer decline towards the grain’s interior, with husk accumulation ranging from 59.1% to 99.95%. Seasonal differences revealed that Si, Mg and Ca accumulated more in the ratoon season, whereas Mn, Cr, Cu, Ni, Co, and Zn were higher in the main season. The content of Mg, Si, Mn, and Zn in the husk varied significantly across ecological conditions and seasons, while other elements showed greater variation in the endosperm. The differences were closely linked to the element’s transport abilities. Transport coefficient indicated stronger movement of Ni across grain parts during the ratoon season, and the enhanced transfer of Mg, Cu, Zn, As, and Cd from the husk to the bran. Moreover, the main season rice could transport and retain Cd in the endosperm more effectively. Principal component analysis revealed positive correlation among Mg, Zn, and Cu in the bran; Ca, Si, Mn, Fe, Cr, and Co in the husk; and toxic elements Pb and Ni. In conclusion, most elements have similar distribution patterns across different rice seasons, ecological conditions, and different parts of the rice grain. The main season has a greater effect on the content and accumulation of elements in different parts of the plant than the ratoon season. Bran is rich in toxic (As, Cd) and beneficial (Mg, Zn, Cu, Se) elements. The transport of elements from the husk to the bran and the processing accuracy of rice are key factors that determine the elemental content in the edible parts of rice. It is recommended that more brown rice should be consumed daily to increase the intake of trace elements required by the human body, whereas in areas with heavy metal contamination, consuming highly polished rice can help reduce exposure to heavy metals and ensure human health and safety.