3D printed short carbon fiber reinforced thermoplastic (SCFRTP) composites are attracting intensive attention because of their advantages such as easy molding, recyclability, etc. The microstructure characteristics including the internal defects, and fiber distributions of 3D printed SCFRTP composites have significant impacts on their performances. In this work, the special engineering plastic polyetheretherketone (PEEK) was used as the matrix, and the 3D printed SCFRTP composites with the short carbon fiber contents of 1 wt% to 10 wt% were prepared and characterized. Then, the probability density distributions of short carbon fibers and micro-void defects were calculated. The micro influencing factors on the tensile properties of the 3D printed SCFRTP composites were studied. This paper provides experimental data for the in-depth analyses and design of 3D printed SCFRTP composites.