Abstract Full-field optical morphology measurement methods are widely used in the shape measurement of underwater targets. The existing models and calibration methods in air could be invalid due to the refraction of light. To deal with these problems, this paper develops a cross-medium imaging model and a relative calibration method. In the modeling, the actual refraction optical path is considered when using arbitrary transparent structures. In the calibration, the accurate parameters of the model are first determined in the air environment and then updated by the refraction index replacement strategy. By using these methods, the accurate restoration of the morphology of objects in any medium is realized, and the inconvenience of underwater calibration process in prior methods can be avoided. The results of conducted experiments show that the accuracy of measurement can achieve 0.42%, which illustrates the validity of the proposed model and the precision of the proposed calibration method.