This study investigates the establishment and calibration method of the rut depth (RD) prediction model of inverted asphalt pavements (IAPs), based on full-scale accelerated pavement testing (APT), which facilitates the accurate and reliable design or maintenance of IAPs. A power function is adopted for the prediction model construction of the rut progression before the failure stage, based on the typical permanent deformation progression curve of flexible pavements. The APT loading history is divided into units, according to the difference in physical conditions, providing the basis for a cumulative RD analysis and model calibration. The nonlinear incremental recursive (IR) principle is applied in the RD analysis to consider the influence of the nonlinear material property, performance deterioration, and loading history on the RD development. Further, the rut shift function relating prediction models obtained from laboratory tests and full-scale APT is established to introduce the APT data in the calibration process. Accordingly, the mechanistic-empirical RD prediction model calibration method, based on APT and the IR principle, is proposed and applied in a case study of a IAP RD prediction model calibration. Four 3.5 m × 4 m IAP test sections S1–S4 are constructed and instrumented and 700,000- and 900,000-wheel loads are applied on test sections S1–S2 and S3–S4, respectively, using the heavy vehicle simulator. The test data from the different APT load units are utilized for the model calibration, and the resultant prediction errors range from −2.16 mm to 1.18 mm. The calibrated model can also be used for the RD prediction of IAPs with other design schemes, by updating the corresponding material-related coefficients and the finite element model, which is essential for the design and maintenance of IAPs. The proposed calibration method could be a useful reference for the establishment of flexible pavement performance prediction models.