Objective：To establish an effective and practical method to solve the problem of polymerase chain reaction（PCR）contamination and used it for prenatal diagnosis of folic acid utilization capability. Methods：By adding recognition sequence of a restriction enzyme FOK1 at the 5′ end of one PCR primer，carryover PCR contamination was controlled by adding FOK1 enzyme in PCR reaction mixture which contained the contamination from the last PCR products. Effects of the amount of FOK1 enzymatic on amplification efficiency，components in PCR reaction mixture and the most amounts of contamination which can be controlled were investigated. A mutation of C677T in MTHFR gene was analyzed. Results：A best reaction system provided by FOK1 enzyme specification inhibited PCR amplification. In TaKaRa reaction system，0.5 U of FOK1 enzyme could completely control the contamination of less than 0.1 μL of last amplification products and did not affect the amplification. Otherwise，false positive results were obtained by adding the contamination without FOK1 enzyme. The developed method was successfully applied to the analysis of MTHFR C677T by sequencing. Conclusion：This method is effective and convenient. The reactions of enzyme digestion and amplification were completed in an unclosed tube. Subsequent sequencing reaction is not affected by the method. The method can not only be used in prenatal diagnosis based on PCR amplification，but also widely applied to control PCR amplification in all the fields involved in nucleic acid amplification.