An apparatus for amplifying nucleic acids includes a substrate, a reaction vessel formed inside of the substrate, at least one first inlet channel formed inside the substrate, connected to an end of the reaction vessel, and allowing introduction of a reactant aqueous solution containing reactants for nucleic acid amplification into the reaction vessel, a second inlet channel formed inside the substrate, connected to the end of the reaction vessel, and allowing introduction of a fluid that is phase-separated from the reactant aqueous solution and does not participate in amplification reaction into the reaction vessel, and a heating unit installed on the substrate in such a way to thermally contact with the substrate and heating the substrate, wherein the reactant aqueous solution contacts the fluid to create a plurality of droplets surrounded by the fluid in the reaction vessel and the nucleic acids are amplified in the reactant aqueous solution droplets.