The Cu2ZnSnSe4 (CZTSe) absorber layer is typically prepared by post-selenization with a metal precursor. In the process of selenization, the loss of SnSex is a common phenomenon, resulting in both an atomic- ratio change and double-layer distribution of the absorber layer. This change affects the film properties. Additionally, excessive deviation from stoichiometry causes the formation of secondary-phase compounds. Moreover, the double-layer distribution reduces the carrier transport between the Mo back electrode and the CZTSe absorber film, inhibiting the effectiveness of the CZTSe solar cell. To address these problems, this study used CuxSe and ZnxSn1−x targets as the sputtering target materials to reduce the loss of SnSex during the selenization of precursor films. In addition, the effect of heating rate on the atomic ratio of the absorber layer was explored by adjusting the heating rate, which is one of the selenization parameters. The results showed that faster heating rates reduced the loss of SnSex, adjusted the Zn/Sn ratio in the absorber layer, and decreased ZnSe-related defects. In this way, the double-layer distribution was improved, air holes were reduced, and crystal structure characteristics of the films were enhanced. Photoluminescence (PL) spectroscopy showed that the signal of the ZnSe-related defect decreased, and the band tail effect became insignificant. The CZTSe absorber layer fabricated under different heating rates is used to prepare the CZTSe solar cell with a photoelectric conversion efficiency ranging from 0.51% to 5.6%.