Active remote sensing technology represented by multi-beam and lidar provides an important approach for the effective acquisition of underwater coral reef geomorphological information. A spatially continuous surface model of coral reef geomorphology reconstructed from active remote sensing datasets can provide important geomorphological parameters for the research of coral reef geomorphological and ecological changes. However, the surface modeling methods commonly used in previous studies, such as ordinary kriging (OK) and natural neighborhood (NN), often represent a “smoothing effect”, which causes the strong spatial variability of coral reefs to be imprecisely reflected by the reconstructed surfaces, thus affecting the accurate calculation of subsequent geomorphological parameters. In this study, a spatial variability modified OK (OK-SVM) method is proposed to reduce the impact of the “smoothing effect” on the high-precision reconstruction of the complex geomorphology of coral reefs. The OK-SVM adopts a collaborative strategy of global parameter transformation, local residual correction, and extremum correction to modify the spatial variability of the reconstructed model, while maintaining high local accuracy. The experimental results show that the OK-SVM has strong robustness to spatial variability modification. This method was applied to the geomorphological reconstruction of the northern area of a coral atoll in the Nansha Islands, South China Sea, and the performance was compared with that of OK and NN. The results show that OK-SVM has higher numerical accuracy and attribute accuracy in detailed morphological fidelity, and is more adaptable in the geomorphological reconstruction of coral reefs with strong spatial variability. This method is relatively reliable for achieving high-precision reconstruction of complex geomorphology of coral reefs from active remote sensing datasets, and has potential to be extended to other geomorphological reconstruction applications.