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Based on the volume magnetic susceptibility and specific gravity measurements and mineral and lithologic identification results for 540 samples, the rock type, density, and magnetic susceptibility of rocks from northern Borneo were analyzed, and the applicability of gravity and magnetic data to the lithologic identification of the Mesozoic strata in the southern South China Sea was assessed accordingly. The results show that there are 3 types and 25 subtypes of rocks in northern Borneo, mainly intermediate-mafic igneous rocks and exogenous clastic sedimentary rocks, with small amounts of endogenous sedimentary rocks, felsic igneous rocks, and metamorphic rocks. The rocks that are very strongly–strongly magnetic and have high–medium densities are mostly igneous rocks, tuffaceous sandstones, and their metamorphic equivalents. The rocks that are weakly magnetic-non-magnetic and have medium–very low densities are mostly conglomerates, sandstones, siltstones, mudstones, and coal. The rocks that are weakly magnetic-diamagnetic and have high-medium densities are mostly limestones and siliceous rocks. The Cenozoic rocks are characterized by low densities and medium susceptibilities; the Mesozoic rocks are characterized by medium densities and medium–high susceptibilities; and the pre-Mesozoic rocks are characterized by high densities and low magnetism. Based on these results and the distribution characteristics of the various rock types, it was found that the pre-Mesozoic rocks produce weak regional gravity anomalies; the Mesozoic sedimentary rocks produce negative regional gravity anomalies; whereas the Mesozoic igneous rocks produce positive regional gravity anomalies; and the Cenozoic igneous rocks produce positive regional gravity anomalies. The regional high magnetic anomalies in the southern part of the South China Sea originate from the Mesozoic mafic igneous rocks and their metamorphic equivalents; and the regional medium magnetic anomalies may be produced by the felsic igneous rocks and their metamorphic equivalents. Accordingly, the identification of the Mesozoic lithology in the southern South China Sea shows that the Mesozoic sedimentary rocks are distributed over a large area of the southern South China Sea. Thus, it is concluded that the Mesozoic strata in this area have the potential for oil and gas exploration.