Scanning probe microscopy (SPM) has demonstrated its exceptional capability in probing the local physical properties of materials. Recent advancements in scanning probe techniques, especially in their integration with electronic devices samples, have significantly broadened their applicability for investigating the microscopic nature of both two-dimensional materials and devices. It facilitates precise control over the system’s physical parameters during measurement, enabling the in operando characterization of the system’s microscopic behavior. Notably, the combination with scanning tunneling microscopy (STM), which detects the energy-dependent electronic structure, allows for the analysis of electronic features while tuning the carrier density of the system. This capability has made device-SPM a powerful tool for studies on topological and correlated quantum phases, enabling the distinction of many-body effects from single-particle features and the characterization of topological invariants of the system. With this state-of-the-art local characterization technique, we focus on investigating the microscopic nature of quantum phases in various low-dimensional materials and nanodevices. We also aim to develop advanced scanning probe microscopy techniques that enable the detection of multiple properties of these systems, thus facilitating a deeper understanding of quantum phenomena.