Carrier doping of MoS2 nanoflakes was achieved by functional self-assembled monolayers (SAMs) with different dipole moments. The effect of SAMs on the charge transfer between the substrates and MoS2 nanoflakes was studied by Raman spectroscopy, field-effect transistor (FET) measurements, and Kelvin probe microscope (KFM). Raman data and FET results verified that fluoroalkyltrichlorosilane-SAM with a large positive dipole moment, acting as hole donors, significantly reduced the intrinsic n-doping characteristic of MoS2 nanoflakes, while 3-(trimethoxysilyl)-1-propanamine-SAMs, acting as electron donors, enhanced the n-doping characteristic. The additional built-in electric field at the interface between SiO2 substrates and MoS2 nanoflakes induced by SAMs with molecular dipole moments determined the charge transfer process. KFM results clearly demonstrated the charge transfer between MoS2 and SAMs and the obvious interlayer screening effect of the pristine and SAM-modified MoS2 nanoflakes. However, the KFM results were not fully consistent with the Raman and FET results since the externally absorbed water molecules were shown to partially shield the actual surface potential measurement. By eliminating the contribution of the water molecules, the Fermi level of monolayer MoS2 could be estimated to modulate in a range of more than 0.45-0.47 eV. This work manifests that the work function of MoS2 nanoflakes can be significantly tuned by SAMs by virtue of affecting the electrostatic potential between the substrates and MoS2 nanoflakes.