An anomalous different threshold voltage shift between P-channel metal-oxide-semiconductor field effect transistor (P-MOSFET) and N-channel MOSFET under high temperature rapid thermal annealing (RTA) borophosphosilicate glass reflow has been studied using 1 μm n+ polygate complementary MOS technology. The boron transient enhanced outdiffusion and phosphorus pileup at channel surface, as well as the interface states generated due to the degradation of thin gate oxide under high RTA process, are proposed as the main sources of this anomalous shift. A detailed model is proposed to interpret the mechanism and some methods to solve the anomalous shift are suggested.