The invention relates to self-alignment channel doping for restraining a CMOS (Complementary Metal Oxide Semiconductor) short channel effect and a preparation method thereof, which solve the following problems in the prior art: 1, doping of a source and a drain is compensated to cause the increase of parasitic resistances of the source and the drain; 2, profiles of PN junctions of a source substrate and a drain substrate are influenced to cause the increase of reversed biased leakage current of the source substrate and the drain substrate; and 3, the junction depth Xj of the PN junctions of the source substrate and the drain substrate can be increased to cause counteractive on the restraint on the SCE (Short Channel Effect). According to the self-alignment channel doping for restraining the CMOS short channel effect and the preparation method thereof, disclosed by the invention, self-alignment doping on CMOS device channel regions is realized, a heavy-doped buried layer under a channel is formed, and source and drain regions are not influenced, thus the SCE is effectively restrained, and the performances of devices are improved.