In September and October of 2011, a marine magnetic survey was conducted in the southern East China Sea between 120° and 126°E, 26° and 28°N with the research vessel Kexue-3. New magnetic maps with 5 × 5 km grid spacing were generated after meticulous data processing. Based on an analysis of magnetic anomaly features and further calculation results, including the total horizontal derivatives (THD), second order vertical derivatives (SVD) and analytic signal amplitude (ASA), several new tectonic insights on magnetic sources, basement structures and fault properties were obtained. The NE-SW or NNE-SSW oriented magnetic anomaly highs have different sources: (1) The high amplitude, short wavelength magnetic anomalies of the Zhemin Uplift are caused by shallow buried igneous rocks intruded along NE-NEE oriented faults. (2) The high amplitude, moderate wavelength magnetic anomalies of the Diaoyudao Uplift are caused by the metamorphic basement intruded by magmatic rocks. (3) The magnetic sources of the Yandang Uplift and Taibei Uplift in the shelf basin are shallow buried metamorphic basements and deep buried volcanic bodies, respectively. Several NW-SE or NWW-SEE oriented dextral strike-slip fault belts were identified as important tectonic boundaries. Each is composed of several en echelon and partly overlapping secondary faults. Initially formed in the Cretaceous, these fault belts have evolved through multiple periods, propagated seaward with the migration of the basement rifting and accommodated local stress fields in the Cenozoic.