Electrostatic force microscopy (EFM) is an emergent, powerful technique for nanoscale detection of electrical properties such as permittivity and charge distribution. However, the surface irregularity of samples has been unfortunately overlooked in most EFM studies. Herein, we use a polymer nanocomposite dielectric (PND) as the showcase and demonstrate that the morphological discontinuity at the matrix/particle interface can lead to major discrepancies or even incorrect results in the EFM study. First, the influence of the morphology, permittivity, and charge density of the interface is quantitively analyzed with a numerical method, proving that linking EFM results directly to sample properties is impracticable in the research based on classical interface configuration. Then, two methods are proposed to address the issue. The first method is numerical inversion, which takes heterogeneous materials and irregular surfaces into consideration. In this method, the influence of several experimental uncertainties, such as the radius of the nanoparticle and the permittivity of the matrix, is estimated. It is shown that the uncertainties related to geometry have a great impact on inversion and should be determined preferentially. In the second method, two standard configurations of the interface are recommended and compared for the interface study to bypass the morphological issue. This work provides quantitative results regarding the longoverlooked error in the EFM detection of the microregion with heterogeneous composition and surface irregularities and offers methods to tackle this issue.