Carbon fiber-reinforced polyetheretherketone (CF-PEEK) composites are highly valued in aerospace and biomedical industries because of their outstanding physical and mechanical properties. However, when made using the Material Extrusion (ME) method, these composites often have insufficient interlaminar shear strength (ILSS) due to their layered structure. This study examines the ILSS of CF-PEEK composites fabricated by the ME technique using two different layer heights under high temperatures. Short beam shear (SBS) tests were conducted to measure the ILSS of 3D-printed CF-PEEK composites. Digital image correlation (DIC) was utilized to capture full-field strain, enabling the observation of failure mechanisms. The findings reveal three main points: firstly, at room temperature, a shorter layer height of 200 µm leads to nearly a fourfold increase in ILSS compared to a 400 µm layer height. Secondly, at a layer height of 400 µm, higher temperatures result in increased ILSS, indicating better adhesion between layers at elevated temperatures. Lastly, at a layer height of 200 µm, higher temperatures significantly improve ILSS, causing a shift in failure mode from interlaminar shear failure to failure caused by bending stress resulting from improved ILSS. These findings suggest the potential to manufacture CF-PEEK composites with enhanced ILSS, thereby enhancing structural reliability for applications requiring superior performance at elevated temperatures.