The In-doped Cd0.9Zn0.1Te (CZT) crystals were grown by the modified Vertical Bridgeman method and treated by in-situ annealing with six different cooling rates. Photo-Induced Transient Spectroscopy (PICTS) and IR microscopy were employed to investigate the evolution mechanism of point defects and bulk defects (mainly Te inclusions) in the CZT crystals with different cooling rates. Related optical and electrical properties were investigated by Fourier Transform Infrared Spectrometer (FTIR) and I–V measurements. The results indicated that cooling at slow rate (10–20 K/h) could decrease the concentration of point defects, such as A center, Cd vacancy , Te antisite and so on, while the Te inclusions are of larger dimension and lower concentration. Otherwise, the faster cooling rate (50–60 K/h), the higher concentration of these point defects, and Te inclusion present small size but much larger concentration. Moreover, cooling too fast or too slow significantly degrades the optical and electrical properties. When cooled at 30–40 K/h, the concentration of internal point defects is the lowest, suggesting that compensated with to reach a new equilibrium corresponding to the theory of quasichemical defect reactions (QCDR). In addition, a certain concentration of was beneficial to pin the Fermi-level, and the Te inclusions presented lowest total volume fraction, which made the crystals perform great with higher resistivity and infrared transmittance.