In order to understand the characteristics of magnetic variability and their possible implication for sub-sea methane venting, magnetic susceptibility (MS) of 145 surface sediment samples from the southern South China Sea (SCS) was investigated. Magnetic particles extracted from 20 representative samples were also examined for their mineral, chemical compositions and micromorphology. Results indicate that MS values range between -7.73x10(-8) and 45.06x10(-8) m(3)/kg. The high MS zones occur at some hydrocarbon-bearing basins and along main tectonic zones, and low ones are distributed mainly within the river delta or along continental shelves. Iron concretions and manganese concretions are not main contributors for high MS values in sediments, while authigenic iron sulphide minerals are possibly responsible for the MS enhancement. This phenomenon is suspected to be produced by the reducing environment where the high upward venting methane beneath the seafloor reacts with seawater sulfate, resulting in seep precipitation of highly susceptible intermediate mineral pyrrhotite, greigite and paramagnetic pyrite. It suggests that MS variability is possibly one of the geochemical indicators for mapping sub-sea zones of methane venting in the southern SCS.