The 3D printing of polyether ether ketone (PEEK) composite of lightweight, high strength, and relatively low-cost composite are rare. This is due to the high melting temperature and poor adhesion problems. This research carefully examines the computational characterization of the nanos-tructure and finite element analysis (FEA) of PEEK/hydroxyapatite (HAP)/-graphene oxide (GO) to solve the problems of high melting temperature and poor adhesion and makes it possible to achieve the lightweight characteristic. Based on the loading condition, a new principal stress trajectory is generated through FEA and used as the guidance for the placement path of PEEK/HAP/GO. The design of the hot extrusion head was implemented at the ambient temperature. Many essential factors were considered while printing PEEK/HAP/GO structures without distortion and degradation of the composite. Compression and traction tests were performed to investigate the mechanical properties of the new PEEK/HAP/GO structure. These were done using three-point flexure test techniques. The addition of physiologically active substances such as bioglass and the incorporation of porosity in PEEK/HAP/GO have been identified as an effective way to improve the osseointegration of bone-implant interfaces, produce a lightweight structure, and improve the biocompatibility of product. A 3000 mm/min printing speed was observed in the 3D-printed PEEK/HAP/GO, with a porosity of 1.2% of maximum increasing strength. This article will help researchers to strengthen their conceptual and computational knowledge of 3D printing tools and medical devices as well as explore future possibilities based on the use of PEEK/HAP/GO.