It is necessary to predict the manoeuvring performance of a submarine accurately at the early design stage for its safe and effective operations. In this paper, the practical 6-DoF simulation models of an X-form stern plane submarine operating near the free surface are proposed. A 1/15 scaled model of ‘BB2 submarine’ is constructed, the captive model tests are performed in a towing tank of Korea Research Institute of Ships and Ocean Engineering (KRISO) at the full-scale depths, 30, 15.4 (snorkel depth), and 4.5 metres (surfaced depth). Resistance and propulsion tests are performed at the deepest depth, 30 metres. The vertical planar motion mechanism (PMM) tests including the forced rolling motions are also carried out at the depth of 30 metres. The horizontal PMM tests are conducted at three kinds of depths, respectively. The depth-varying horizontal plane coefficients in the model are identified, and the coefficients which are little influenced by the depths are treated as the constant values for the practical purpose. Some of velocity coupled terms are approximated by using the added mass coefficients on the assumption that the viscous components are negligible. In addition, the resistance increases, vertical suction forces and moments are measured in the straight-ahead tests with varying the submergence depths. The free surface effects are considered as the exponential function terms in the proposed models. Based on the present tests and the previous studies about the free surface effects on the submerged bodies, it is practically assumed that the free surface effects are exponentially decayed with the depths, and are already negligible when the submergence depth is 30 metres, approximately three times the hull depth. Horizontal and vertical plane manoeuvring motions as well as the neutral flights are simulated with the control plane deflections less than 15 degrees. The present simulations are in good agreements with existing free-running model test results.