The radiation-induced charge distribution in shallow-trench isolation (STI) structures is analyzed in this paper. We present a new approach for modeling total dose effect of ultra-deep submicron transistors. The results show that, when there is no radiation-induced charge in top100 nm of the trench-silicon interface, the simulation results of 0.18μm ultra-deep submicron transistors show that the I-V sub-threshold does not produce the hump, and yield good agreement with experiments. On the aspect of the improvement on total ionizing dose, the leakage current of MOSFET with delta doping can be effectively reduced than with the uniform doping profile under lower radiation dose. If the Halo doping is adopted in landscape orientation, the total dose of ultra-deep submicron transistors can be improved. This improvement is evident even at higher irradiation dose.