A wavelength conversion element manufacturing method capable of realizing, in a wavelength conversion element having a structure in which a thin film substrate having a periodic polarization inversion structure and a support substrate are laminated, highly efficient wavelength conversion by confining light in a cross-sectional area smaller than in the known art. The manufacturing method includes steps of forming a periodic polarization inversion structure on a first substrate made of a second-order nonlinear optical crystal and forming a damage layer in the first substrate by implanting ions from one substrate surface to obtain a first substrate for bonding, directly bonding a second substrate having a bonding surface having a smaller refractive index than the first substrate to the one substrate surface of the first substrate at the bonding surface, and peeling the first substrate directly bonded to the second substrate being the support substrate with the damage layer as a boundary to remove a part of the first substrate.