Gas turbines are widely used in power generation, aviation, and clean energy utilization. The accuracy of the overall performance prediction is of great importance when designing gas turbines. The purpose of this study is to develop a full-engine throughflow simulation method based on a time-marching scheme to obtain a more accurate prediction of gas turbine performance. To precisely calculate the flow deflection inside the blades, a robust inviscid blade force model was established using a theoretical derivation. The results indicate that in transonic flow, the blade force model can deteriorate the conservation of the throughflow governing equations during the time-marching process. To overcome this issue, a quasi-orthogonal body-fitted coordinate system was adopted based on theoretical analysis. Subsequently, a viscous force model coupled with a variety of empirical models was introduced to simulate the viscous effects. A simple but effective way of distributing the fuel source terms in the combustion area was employed to simulate the burning process. Finally, the developed throughflow method was applied to conduct flow simulations of the KJ66 micro gas turbine engine. The predicted overall performance matched well with the experimental data, with a maximum error of less than 6.48% among the comparisons of thrust, specific fuel consumption, and exhaust gas temperature; furthermore, the proposed method was more accurate than the traditional thermal cycle calculation. The novelty of the present study lies in the time-marching solution of the full-engine throughflow simulation and its ability to eliminate the dependence on the generic component map and obtain meridional distributions of the flow parameters. The results can offer valuable guidelines for the integrated design and optimization of components in Brayton cycles. • A strictly conservative throughflow model is developed for gas turbine simulation. • The full-engine throughflow simulation of micro gas turbine is achieved. • Throughflow model can eliminate the dependence on generic map of components. • Throughflow model can improve off-design performance prediction for gas turbine. • Throughflow model can obtain meridional details of flow parameters in gas turbine.