An ultra-low thermal budget process is provided for channel implant by using a reverse process sequence where a conventional MOS transistor is formed without the channel implant. The originally deposited polysilicon gate is removed, a nitride film deposition and etch is used to form a nitride spacer with a predetermined configuration, and a self-aligned channel implant is performed. After the channel implantation, anneal and super-retrograded doping, the nitride spacer and the gate oxide are removed for subsequent regrowth of a second gate oxide and a polysilicon deposition to form a second polysilicon gate.