The growth mechanism of Cd doped ZnSe quantum dots (QDs) obtained from the aqueous synthesis method is studied by in situ X-ray absorption fine structure (XAFS), UV-vis absorption spectra and photoluminescence (PL). Detailed analysis reveals that just after the injection of Cd ions into ZnSe QDs precursor, the Cd ions are immediately deposited on the surfaces of the ZnSe QDs, and enter the lattice of ZnSe QDs, cause the distortion of lattice. With heating, the surface defects remove from the QDs, but the distortion of Cd doped ZnSe QDs lattice still aggravates in the initial 30min. After 120min of heating, the surfaces of the Cd doped ZnSe QDs are well passivated by glutathione capping, and the lattice defects of the QDs also decrease along with further growth of the QDs.