A process for preparing a fluorine-containing polymer through emulsion polymerization method which enhances productivity while maintaining excellent physical properties of the fluorine-containing polymer and comprises (a) a first polymerization step for emulsion-polymerizing a fluorine-containing monomer or a mixture of a fluorine-containing monomer and a non-fluorine-containing monomer in an aqueous medium in the presence of a radical polymerization initiator and an emulsifying agent, (b) a dilution step for diluting the obtained aqueous emulsion of polymer particles with water to reduce the number of emulsified polymer particles per unit amount of aqueous medium in the emulsion and a concentration of emulsifying agent, and (c) a second polymerization step for emulsion-polymerizing a fluorine-containing monomer and/or a non-fluorine-containing monomer in the obtained diluted emulsified solution.