An object of the present invention is to provide a method of manufacturing a composite substrate including a piezoelectric layer with less Li amount variation and a support substrate. A method of manufacturing a composite substrate of the present invention includes a step of performing ion implantation into a piezoelectric substrate, a step of bonding the piezoelectric substrate and the support substrate, a step of separating the bonded substrate, at an ion-implanted portion of the piezoelectric substrate, into the piezoelectric layer bonded to the support substrate and the remaining piezoelectric substrate after the step of bonding the piezoelectric substrate and the support substrate, and a step of diffusing Li into the piezoelectric layer after the separating step.