Provided is a method of producing 1,3-propanediol by culturing a recombinant strain in which the glycerol oxidative pathway had been blocked, and more particularly a method of producing 1,3-propanediol by two-step culture of a recombinant strain in which the oxidative pathway that produces byproducts in the glycerol metabolic pathway had been blocked. When the recombinant strain in which the glycerol oxidative pathway that produces byproducts had been blocked is cultured in two steps, 1,3-propanediol can be produced with improved yield without producing products that result in an increase in purification costs.