A tunable graphene doping method utilizing a SiO2/Si substrate with nanopores (NP) was introduced. Laser interference lithography (LIL) using a He–Cd laser (λ = 325 nm) was used to prepare pore size- and pitch-controllable NP SiO2/Si substrates. Then, bottom-contact graphene field effect transistors (G-FETs) were fabricated on the NP SiO2/Si substrate to measure the transfer curves. The graphene transferred onto the NP SiO2/Si substrate showed relatively n-doped behavior compared to the graphene transferred onto a flat SiO2/Si substrate, as evidenced by the blue-shift of the 2D peak position (∼2700 cm−1) in the Raman spectra due to contact doping. As the porosity increased within the substrate, the Dirac voltage shifted to a more positive or negative value, depending on the initial doping type (p- or n-type, respectively) of the contact doping. The Dirac voltage shifts with porosity were ascribed mainly to the compensation for the reduced capacitance owing to the SiO2–air hetero-structured dielectric layer within the periodically aligned nanopores capped by the suspended graphene (electrostatic doping). The hysteresis (Dirac voltage difference during the forward and backward scans) was reduced when utilizing an NP SiO2/Si substrate with smaller pores and/or a low porosity because fewer H2O or O2 molecules could be trapped inside the smaller pores.