Chemical vapor deposition graphene (CVDG) and electrochemical exfoliated graphene (ECG) were transferred and spin-coated on the nanoporous alumina substrate (NS) and flat alumina substrate (FS) to investigate the effect of substrate topography for graphene-based humidity sensors. The electrical resistance change of two graphene types on different substrate topography could be measured to estimate the environmental relative humidity. The relationship between graphene types, substrate topography, wettability, and humidity sensing performance was studied and discussed. The results of the water contact angle of CVDG on NS/FS and ECG on NS/FS were 77.0 ± 5.0°, 88.8 ± 4.9°, 55.9 ± 7.0°, and 59.8 ± 3.2°, respectively. The response, linearity and hysteresis characteristics of four graphene-based humidity sensors were measured and estimated. The ECG on NS humidity sensor shows the best performance in regards to the response, linearity and hysteresis.