•Organic molecules induced doping in atomic layer materials formed on solid surfaces•Controlling the charge states by the coverage of organic molecules•Manipulating the Tc of atomic layer superconductors with organic molecules Display omitted In/Si(111)-(7×3) is an atomic layer superconductor formed by an In double layer on Si(111). The size of its circular Fermi surface becomes smaller by the adsorption of copper-phthalocyanine (CuPc) molecules till a coverage of 1.0 monolayer, and then larger at higher coverage. This means that it is possible to control the amount of hole doping, and therefore to tune the energy of the band by CuPc adsorption. By comparing the change in transition temperature (Tc) reported in “Nano Lett. 17 (2017) 2287”, whose reports the manipulation of Tc by CuPc adsorption, and the behavior of the Fermi surface observed in the present study, we conclude that both the increase of Tc till a CuPc coverage of 1.0 ML and its decrease from 1.0 to 2.0 ML have strong correlations with the amount of hole doping from CuPc to In/Si(111)-(7×3).