Provided is a method of purifying a target substance using silver nanoparticles. The method includes: mixing a sample containing molecules having a thiol group with the silver nanoparticles to obtain a complex of the molecules having the thiol group with the silver nanoparticles; and isolating and removing the complex from the mixture. By using the purification method, PCR amplifiable DNAs can be rapidly purified, and thus, the method can be very efficiently applied to lab-on-chip (LOC).