The bioleaching behaviors of chalcopyrite with two different metallogenic types by iron- and sulfur-oxidizing Sulfobacillus thermosulfidooxidans were investigated. It was found that the skarn-type chalcopyrite (STC) exhibited much faster leaching rate and the copper extraction was 33.34% after 21 days of biooxidation, while that of the porphyry-type chalcopyrite (PTC) was only 23.53%. The reasons were explained from the perspective of mineralogy. The analysis of XRD indicated that STC had slightly larger cell parameters than PTC. More stepped and bulgy structures were observed on the STC surface, as displayed in SEM images. The XPS spectra showed that copper on the surfaces of the two types of chalcopyrite mainly existed in the form of Cu(I), and STC had much higher copper content and lower Cu 2p3/2 binding energy than PTC. These differences in mineralogy resulted in the more excellent bioleaching kinetics of STC. This study is pretty useful in understanding the relation between the bioleaching behaviors of chalcopyrite and the mineralogical properties.