The Yimen Fengshan copper deposit is a typical Yimen-type copper deposit which is located in the copper mineralization belt of the Kunyang rift valley, Yunnan Province, China. The paper researched the 59# orebody area based on tectono-geochemistry. By R-cluster analysis and R-factor analysis, the authors got six and seven factors respectively, summed up the anomaly features and their regularities of distribution. The metallogenic elemental assemblage anomaly is located in the same position as 59# orebody, appears at the margin of the diapiric structure; the presence of (Bi-Cu), (TFe-W-Mo-Cu-Bi) and (Zn-Cd-Cu-Ag-Pb-Bi-Mo) ore-forming factors’ anomaly superposition indicated that the deposit had undergone superimposed mineralization. The paper speculated ore fluids migrated from the diapiric structure to wall rocks, and ore occurrence by anomaly features and its regularities of distribution, the result plays an important role for the depth ore-finding prognosis.