Abstract: The elemental composition of a subcellular compartment, cell, tissue or organism is termed as ionome, which involves of all mineral elements of life, regardless of chemical forms these occur. Ionome is the inorganic chemical element fingerprint of plant that quantitatively and accurately reflects inorganic response of plants to environment stimuli. A field experiment was conducted to explore the differences and correlations of mineral elements in rice seeds cultivated in conventional cultivation ecosystem, green rice-frog ecosystem and organic rice-frog ecosystem under long-term management. The study also determined the transportability of available elements from soil to rice seeds to explore the correlation of elements between soil and rice seed effects of rice cultivation pattern on seed ionome. The concentrations of 21 mineral elements in the rice samples and soil were determined using high-throughput elemental analysis technology such as inductively coupled plasma optical emission and mass spectrometry (ICP-MS). Statistical method used to profile multi-elemental composition, and principle component analysis (PCA) to discriminate differences among treatments was principle component analysis (PCA). Then ANOVA analysis was used to compare the differences among treatments for each element. The results showed the ranked order of the concentrations of 21 elements in rice seeds was: potassium (K) > phosphorus (P) > magnesium (Mg) > calcium (Ca) > manganese (Mn) > zinc (Zn) > ion (Fe) > copper (Cu) > rubidium (Rb) > sodium (Na) > barium (Ba) > molybdenum (Mo) > boron (B) > nickel (Ni) > strontium (Sr) > arsenic (As) > chromium (Cr) > cadmium (Cd) > selenium (Se) > cobalt (Co) > cesium (Cs). PCA analysis showed that ionome of rice seeds was significantly affected by different cultivation patterns. The fist component accounted for 32.7% of the total variation, which separated organic rice-frog ecosystem from organic rice-frog ecosystem. The second component accounted for 27.1% of the total variation, which discriminated conventional cultivation system from the other two ecosystems. Compared with conventional cultivation, the concentrations of K, Na, Rb and Cs (which belonged to the first group of the periodic table), Mn and Cd in rice seeds significantly increased by 21%, 31%, 59%, 72%, 23% and 441%, respectively, in green rice-frog ecosystem. On the contrary, B and Cr decreased by 63% and 51% under green rice-frog ecosystem. The concentrations of Co, Ni and Cd in rice seeds increased by 60%, 286% and 488%, but Ca, B, Mo, Sr and Cr decreased by 38%, 60%, 20%, 27% and 96% under organic rice-frog ecosystem. However, no competition was observed among element pairs in this study. Moreover, essential elements such as Zn, Cu and P had higher transportability from soil to rice seeds, while non-essential elements such as Na, Ba and Cs had lower transportability from soil to plant. Based on nutrient element accumulation in rice, the study showed that green rice-frog ecosystem was better than both organic rice-frog ecosystem and the conventional cultivation system. However, the uptake and accumulation of some non-essential elements in rice seeds under green rice-frog ecosystem and organic rice-frog ecosystem also put at risk rice crops and food security at risk. Therefore, it was important to improve existing knowledge on scientific management of nutrients as well as reasonable adjustment of planting structures to ensure food security.