Constraining the properties of continental margin where dynamic interplay between the lithosphere and convective upper mantle actively occurs can provide implications to understand the evolution and modification process of cratonic lithosphere. Cratonic lithosphere in the eastern Eurasian plate has experienced multiple episodes of tectonic events at the continental margin during the Phanerozoic, which are characterized by collision and subduction of continental and oceanic plates with extensive magmatic intrusion, extension, and rifting. To better understand the complex tectonic processes and their influences on the continental lithosphere, we imaged upper mantle structure beneath the Archean-Proterozoic basement in the Korean Peninsula (KP) by seismic tomography. Our dataset is entirely based on relative arrival time of teleseismic body wave recorded by dense seismic array across the southern KP in order to extract velocity variations from the local area and reduce the effects from deeper upper mantle structures. The images show a sharp and large lateral velocity variation within a short distance (< 200 km) in KP, which indicates highly variable lithospheric structure. An anomalously thick high-velocity structure beneath the southwestern part suggests a fragment of a long-lasting cratonic lithosphere (~150 km) at the continental margin. The absence of deep lithosphere and mostly occupied by hot, buoyant, low-velocity upper mantle beneath the Gyeonggi massif, Gyeongsang continental arc-backarc system, and eastern continental margin of KP shows highly modified regions. In addition, there are clear spatial correlations of low-velocity upper mantle with partial melting zones and the localities of Cenozoic basalts, high surface heat flux, and high topography with recent uplift along the eastern mountain ranges. A strong variation in the upper mantle velocity structure without clear distinctions in surface geology across different massifs suggests heterogeneous modification of continental lithosphere by recent and transient processes, such as the opening of the East Sea (Sea of Japan) or a subduction of Philippine Sea Plate. Dynamic interaction of the prominent lithospheric structure and convective upper mantle has controlled reactivation and destabilization at the cratonic margin of KP.