Owing to the melting and healing properties of thermoplastic resin, additive manufacturing or 3D printing is considered one of the most promising technologies for fiber-reinforced thermoplastic composites. However, manufacturing defects are still the main concern, which significantly limits the application of 3D-printed composite structures. To gain an insight into the effects of different processing parameters on the typical manufacturing defects, a micro-scale analysis was carried out via Micro-CT technology on the 3D-printed continuous carbon fiber-reinforced polylactic acid (PLA) composite specimens. The bias distribution of the fiber in the deposited filament was found. Moreover, when the feed rate of the filament was reduced from 100% to 50%, the a/b value was closer to 3.33, but the porosity increased from 7.077% to 25.352%. When the layer thickness was 0.2 mm, the increased nozzle pressure reduced the porosity but also increased the risk of fiber bundle breakage. The research provides an effective approach for analyzing the micro-structure of 3D printed composite structures and thus offers guidance for the processing control.