Organic reefs, the targets of deep-water petroleum exploration, developed widely in Xisha area. However, there are concealed igneous rocks undersea, to which organic rocks have nearly equal wave impedance. So the igneous rocks have become interference for future exploration by having similar seismic reflection characteristics. Yet, the density and magnetism of organic reefs are very different from igneous rocks. It has obvious advantages to identify organic reefs and igneous rocks by gravity and magnetic data. At first, frequency decomposition was applied to the free-air gravity anomaly in Xisha area to obtain the 2D subdivision of the gravity anomaly and magnetic anomaly in the vertical direction. Thus, the distribution of igneous rocks in the horizontal direction can be acquired according to high-frequency field, low-frequency field, and its physical properties. Then, 3D forward modeling of gravitational field was carried out to establish the density model of this area by reference to physical properties of rocks based on former researches. Furthermore, 3D inversion of gravity anomaly by genetic algorithm method of the graphic processing unit (GPU) parallel processing in Xisha target area was applied, and 3D density structure of this area was obtained. By this way, we can confine the igneous rocks to the certain depth according to the density of the igneous rocks. The frequency decomposition and 3D inversion of gravity anomaly by genetic algorithm method of the GPU parallel processing proved to be a useful method for recognizing igneous rocks to its 3D geological position. So organic reefs and igneous rocks can be identified, which provide a prescient information for further exploration. Keywords Xisha area Á Organic reefs and igneous rocks Á Frequency decomposition of potential field Á 3D inversion of the graphic processing unit (GPU) parallel processing