Abstract: This paper represents a mathematical model of transpiration cooling control system with two-dimensional heating and surface ablating. Applying time semistep alternating direction method to quantize this mathematical model, the tri-diagonal difference equations are obtained. The mathematical simulation results for the flying shell of the electromagnetic railgun show that the control parameter is effective for the control of temperature field and the boundary motion. The evidence of the analytic character on the mathematical theory is provided from the mathematical simulation. The characteristic of two-dimensional temperature field is given and the problem of the synchronization ablation is discussed.