Purpose <p>Due to the irregularity of cervical inferior endplate morphology among individuals and segments, a bone-implant interface (BII) gap is usually unavoidable between the prosthesis and endplate after cervical disc replacement (CDR). This study aimed to investigate the clinical and biomechanical effects of the BII gap after CDR.</p> Methods <p>We retrospectively reviewed the clinical and radiological data of 180 patients who underwent 1-level or 2-level CDR. Cervical sagittal parameters, implant subsidence and migration, heterotopic ossification (HO) were evaluated through lateral radiographs. Endplate morphology was classified into three types according to the position of concavity apex: (I) posterior, (II) central, and (III) anterior. CDR finite element models with and without BII gap were developed based on type II endplate to analyze predictions of relative stress distributions, micromotions and associated risks for subsidence at BII.</p> Results <p>No statistical differences in clinical outcomes and the incidence of implant subsidence or migration between two groups were noted. The proportion of BII gaps after CDR was significantly larger in segments with type I endplate morphology (68.0%) (<i>P</i> = 0.001). The incidence of HO (67.8% vs. 53.5%, <i>P</i> = 0.026), high-grade HO (21.2% vs. 11.4%, <i>P</i> = 0.044), and posterior HO (63.6% vs. 49.1%, <i>P</i> = 0.027) in the gap group was significantly higher. There were obvious stress concentration areas in the posterior region of the endplate in the gap model. The risk for subsidence of the gap model was larger than non-gap model in flexion, extension, and lateral bending.</p> Conclusion <p>The BII gap was common after CDR. The incidences of posterior HO and high-grade HO were higher in the segments with BII gap. Although the BII gap altered the regional biomechanical environment, no effects on the clinical outcomes and risk for implant-related complications were noted.</p>