The objective of this study was to investigate the difference of chicken from organic and conventional systems. Chicken samples from three farms (Beijing conventional farm, Beijing organic farm, and Jilin organic farm) of each type were measured for contents of protein and fat, stable carbon and nitrogen isotope ratios, and concentrations of 12 mineral elements (Na, Mg, K, Ca, V, Fe, Co, Ni, Cu, Rb, Ba, and Pb). As a result, the chicken of two organic groups (Beijing organic and Jilin organic) yielded more protein than the Beijing conventional group. The nitrogen and carbon stable isotope ratios of de-fatted chicken from organic groups were higher than those of conventional ones. Mineral elements in de-fatted chicken samples showed significant differences (p < 0.05) except for Mg. The analysis data of stable isotope ratios and multielements were subjected to principal component analysis (PCA). The organic and conventional groups can be clearly classified through PCA. The combination of stable isotopes and multi-elements can further classify the geographical origin of chicken. The research work brought about a discovery of the difference between the organic and conventional chicken.