The inferior biocompatibility of the polyethylene terephthalate (PET) artificial ligament may lead to poor healing in both the intra-articular part (IAP) and the intraosseous part (IOP) after anterior cruciate ligament (ACL) reconstruction. This study aimed to systematically investigate the effect of silk fibroin (SF) and hydroxyapatite (HA) segmented coating on graft ligamentization and osseointegration processes of the PET ligament. Several techniques including scanning electron microscopy (SEM) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, X-ray diffraction (XRD) and water contact angle (WCA) measurements were carried out to validate the introduction of SF and HA. The segmented coating ligament was assessed both in vitro and in vivo. The results of SEM and cell counting kit-8 (CCK-8) assay revealed that the L929 fibroblasts and MC3T3-E1 osteoblasts exhibited better adhesion and proliferation performance on the PET–SF and PET–HA fibers, respectively, compared to those on the uncoated PET fibers. HA promoted osteogenic differentiation of MC3T3-E1 in terms of the levels of alkaline phosphatase (ALP) activity and calcium deposition. Furthermore, the in vivo study in a beagle ACL reconstruction model demonstrated that the segmented coating could enhance the graft ligamentization and osseointegration processes as indicated by the better tissue infiltration in the IAP and more bone ingrowth in the IOP of the ligament than the control group according to the results of micro-computed tomography (micro-CT), histology, real-time polymerase chain reactions (RT-PCRs) and biomechanical tests. Therefore, the SF and HA segmented coating ligaments may display a great potential application for the clinical augmentation of graft healing in ACL reconstruction surgery.