We have presented a discrete equivalent source method to perform a stable gravity downward continuation for structural delineation in the Sulu Sea region. Our method automatically selects an effective small amount of the discrete sources by using the modified Blakely and Simpson's method. It tests whether each observed gravity is minimum or maximum relative to the neighbouring eight points, then assigns the coordinates to one discrete source. This procedure reduces the coefficient matrix size. Moreover, the method assumes each source as a point source instead of rectangular prism to reduce model parameters. Then, it iteratively searches an optimum solution and the corresponding depth by simultaneously using both the CG and Golden Section Search algorithms. The optimum solution and the corresponding depth are then used to compute the downward continued gravity field. Testing on synthetic data confirmed the efficiency of our method in performing stable downward continuation. The method is also appropriate for computing gravity upward continuation, potential field on a plane or an uneven surface, and centroid depths of causative sources. A combination of both the downward continuation and an effective boundary detection technique delineated several faults and volcanic/intrusive rocks in the Sulu Sea region. These structure were formed by plate movement, subduction and collision. Finally, the reoriented structures along the dextral strike-slip fault that passes though the Sulu Sea and Sulu ridge was attributed to the increasing speed of the Philippine plate towards the north.