The atomic and electronic structures of pristine PdSe2 as well as various intrinsic vacancy defects in PdSe2 are studied comprehensively by combining scanning tunneling microscopy, spectroscopy, and density functional theory calculations. Other than the topmost Se atoms, sublayer Pd atoms and the intrinsic Pd and Se vacancy defects are identified. Both VSe and VPd defects induce defect states near the Fermi level. As a result, the vacancy defects can be negatively charged by a tip gating effect. At negative sample bias, the screened Coulomb interaction between the scanning tunneling microscopy (STM) tip and the charged vacancies creates a disk-like protrusion around the VPd and crater-like features around VSe. The magnification effect of the long-range charge localization at the charged defect site makes sublayer defects as deep as 1 nm visible even in STM images. This result proves that by gating the probe, scanning probe microscopy can be used as an easy tool for characterizing sublayer defects in a nondestructive way.