Scanning tunneling microscope (STM) provides an atomic-scale characterization tool. To this end, high-resolution measurements and accurate simulations must closely cooperate. Emerging experimental techniques, e.g., substrate spacers and tip modifications, suppress metallic couplings and improve the resolution. On the other hand, development of STM simulation methods was inactive in the past decade. Conventional simulations focus on the electronic structure of the substrate, often overlooking detailed descriptions of the tip states. Meanwhile, the overwhelming usage of periodic boundary conditions ensures effective simulations of only neutral systems. In this Perspective, we highlight the recent progress that takes the effects of both tip and substrate into account under either Tersoff−Hamann or Bardeen's approximation, which provides an accurate analysis of measured high-resolution STM results, uncovers underlying concepts, and rationally designs experimental protocols for important chemical systems. We hope this Perspective will stimulate broad interest in advanced STM simulations, highlighting the way forward for STM investigations that involve complex geometrical and electronic structures.