The present invention provides a kind of new method for being used to prepare cell binding agent cytotoxic agent conjugate. It the described method comprises the following steps: react cell binding agent in the presence of the buffer solution with high ionic strength under the pH between 4 to 9 of cytotoxic agent or cytotoxic agent-linker compounds with the reactive group that can form covalent bond with the cell binding agent, wherein the cell binding agent includes and the cytotoxic agent with amine reactive group or cytotoxic agent-linker compounds form the lysine ε-NH2 groups of covalent bond. The invention also includes the cell binding agent prepared according to method described herein-cytotoxic agent conjugates.