In addition to remote-sensing monitoring, reconstructing morphologic surface models through interpolation is an effective means to reflect the geomorphological evolution, especially for the lagoons of coral atolls, which are underwater. However, which interpolation method is optimal for lagoon geomorphological reconstruction and how to assess the morphological precision have been unclear. To address the aforementioned problems, this study proposed a morphological precision index system including the root mean square error (RMSE) of the elevation, the change rate of the local slope shape (CRLSS), and the change rate of the local slope aspect (CRLSA), and introduced the spatial appraisal and valuation approach of environment and ecosystems (SAVEE). In detail, ordinary kriging (OK), inverse distance weighting (IDW), radial basis function (RBF), and local polynomial interpolation (LPI) were used to reconstruct the lagoon surface models of a typical coral atoll in South China Sea and the morphological precision of them were assessed, respectively. The results are as follows: (i) OK, IDW, and RBF exhibit the best performance in terms of RMSE (0.3584 m), CRLSS (51.43%), and CRLSA (43.29%), respectively, while with insufficiently robust when considering all three aspects; (ii) IDW, LPI, and RBF are suitable for lagoon slopes, lagoon bottoms, and patch reefs, respectively; (iii) The geomorphic decomposition scale is an important factor that affects the precision of geomorphologic reconstructions; and, (iv) This system and evaluation approach can more comprehensively consider the differences in multiple precision indices.