A method of manufacturing a microlens substrate having a plurality of microlenses includes the steps of: preparing a substrate having two major surfaces and a plurality of concave portions formed in one of the two major surfaces, each of the concave portions having a shape corresponding to that of each of the microlenses being formed in the one of the two major surfaces of the substrate; preparing a base material substrate formed of glass having a transformation point lower than that of a constituent material constituting the substrate; and pressure-joining the substrate to the base material substrate in a heating state. In the pressure-joining step, the substrate is joined to the base material substrate and the concave portions fill with the glass material of the base material substrate which is melted by the heat.