Atomic manipulation technique with scanning tunneling microscopy (STM) has been used to control the structural and physical properties of materials at an atomic level. Recently, this technique has been extended to modifying the physical properties of low-dimensional materials. Unlike conventional single atom lateral manipulation, the STM manipulation technique in the study of low-dimensional materials has additional manipulation modes and focuses on the modification of physical properties. In this review paper, we introduce the recent experimental progress of tuning the physical properties of low-dimensional materials through STM atomic manipulation technique. There are mainly four manipulation modes: 1) tip-induced local electric field; 2) controlled tip approach or retract; 3) tip-induced non-destructive geometry manipulation; 4) tip-induced kirigami and lithography. Through using these manipulation modes, the STM tip effectively introduces the attractive force or repulsive force, local electronic field or magnetic field and local strain, which results in the atomically precise modification of physical properties including charge density wave, Kondo effect, inelastic tunneling effect, Majorana bound states, and edge states.