Because of the apparent fusion interface, the Poly Lactic Acid (PLA) parts, obtained by fused deposition modeling 3D printing, have low strength and poor plastic toughness, which limit their applications. In this paper, to focus on the fusion interface bonding properties, firstly, the nano-hydroxyapatite (n-HA) was modified by PLA to obtain a core-shell structure with PLA coating, afterward, the modified n-HA was coated on the surface of the PLA filament by the ultrasonic dipping method to obtain the PLA/n-HA composite filament. Secondly, computational fluid dynamics (CFD) software was used to calculate and analyze the flowing state and printing parameters of PLA/n-HA composites based on the rheological experimental results. Finally, the PLA/n-HA composite tensile samples were manufactured by fused deposition modeling 3D printing, and the tensile test was conducted. The results show that after numerical calculation, the optimized printing temperature and printing velocity of PLA/n-HA composite was 210°C and 90 mm/s, respectively. Meanwhile, the modified n-HA had good dispersibility in the PLA_5% n-HA composite filament (the modified n-HA content is 5%), therefore, the 3D printed parts manufactured by PLA_5% n-HA composite filament obtained the best modified n-HA distribution in the interlayers, and the best reinforcement of interlayer bonding was obtained reasonably.