According to the invention, based on Illumina common tag library sequencing and methylation normal sequencing and combining a common library tag sequencing method, a new method for accurate detection of whole genome methylation sites by utilizing trace genome DNA (deoxyribonucleic acid) is built. According to the method, in the construction of a methylation library by using trace genome DNA, exogenous DNA is innovatively added to carry out bisulfite high-efficiency co-treatment; and at the same time, fragment size selection is not needed, and PCR (polymerase chain reaction) amplification is directly carried out after bisulfite treatment. By the method, the defects that in the common methylation sequencing, samples can not be mixed, the PCR amplification efficiency is low and the trace DNAsample can not be researched are overcome.