Disclosed is a low impurity content caspofungin pharmaceutical composition and a method for preparing the low impurity content caspofungin pharmaceutical composition. The caspofungin pharmaceutical composition comprises the compound of formula I and/or a pharmaceutically acceptable salt thereof, in combination with a saccharide protective agent(s) and an amino acid(s). The caspofungin pharmaceutical composition is prepared by dissolving the saccharide protective agent and the amino acid into water or a suitable buffer solution; adding the caspofungin compound and dissolving it; filtering the solution and lyophilizing.