A method of manufacturing a three-dimensional shaped object, which is a method of shaping a three-dimensional shaped object using a cutting tool configured to cut a first length in a cutting direction, includes: a first portion shaping step of stacking a shaping material to shape a first portion having a length in the cutting direction shorter than the first length; a first portion cutting step of cutting the first portion in the cutting direction by the cutting tool; and a second portion shaping step of stacking the shaping material to couple to a first end surface of the first portion in a direction opposite to the cutting direction, and to shape a second portion having a length in the cutting direction shorter than that of the first portion.