Carbon fiber reinforced poly aryl ether ketone (SCF35/PAEK) thermoplastic composites were prepared using two different melt viscosities of domestic high performance poly aryl ether ketone resins (PAEK-L and PAEK-H) and domestic T300 grade carbon fibers (SCF35), and the effects of resin matrix viscosity and impact energy and impact energy on the impact properties of the composites were investigated. In addition, the internal morphology of quasi-static indentation specimens was characterized by Micro-CT to study the impact damage mechanism of the composites. The results show that PAEK-L resin matrix composite with lower fluidity has higher impact resistance than PAEK-H resin matrix composite with higher fluidity. The impact energy loss of the SCF35/PAEK-L composite system is ~7% lower than that of the SCF35/PAEK-H composite system, its damage area is ~90% smaller, and its compression strength after impact reaches ~307 MPa at an impact energy of 6.67 J/mm, which is ~50% higher than that of SCF35/PAEK-H composite system(205 MPa). The depth of surface dent in SCF35/PAEK-L composites tends to increase with the increase of impact energy, and the compression strength after impact tends to decrease with the increase of impact energy, and the compression strength after impact is ~268 MPa when the depth of surface dent of the composites reaches about 1.0 mm, i.e., when the threshold value of barely visible impact damage (BVID) is reached. In addition, the results of quasi-static indentation tests show that the surface dent of SCF35/PAEK-L composite after impact is mainly caused by plastic deformation of the resin matrix and fiber flexure, the cracks around the surface dent are caused by compressive stress, the fiber on the back side of the specimen is fractured under the action of tensile stress during the impact process, the fiber on the bottom layer of the specimen sprouts interlayer cracks under the action of shear force, with the increase of flexural deformation of the specimen, the degree of fiber fracture increases and the interlayer cracks gradually expand.