In this paper, the interlaminar bond strength of laser in-situ consolidation (ISC) CF/PEEK thermoplastic composites was investigated under different process conditions. Short beam shear (SBS) tests were conducted to characterize the load-displacement response, the trend of interlaminar shear strength (ILSS), and the mechanism of porosity and crystallinity on ILSS. The experimental results show that porosity has a significant effect on ILSS. Although increasing the tool temperature results in a more stable and homogeneous crystal structure, no correlation is observed between crystallinity and ILSS. The highest measured ILSS value in the heated tool in-situ consolidation (HTISC) group is 59.59 MPa. The aforementioned represents an increase of 61.23% compared to the constant pressure in-situ consolidation (CPISC) group. The proposed method can be used to provide a reference value for acceptance criteria in engineering applications of thermoplastic composites.