In order to solve the problem of automatic selection of tracking point in target tracking after automatic target recognition of IR warship targets in the infrared imaging and tracking systems, a new automatic detection algorithm of ship aimpoint was proposed. Based on the waterline′s geometrical relationship below the warship and the high brightness characteristics of engine compartment, the cross part of the waterline and engine compartment was detected. This cross part was taken as the primary aimpoint of IR warship target. Otherwise, the central part of the waterline would be taken as the aim point of IR warship target. First of all, the de-noising pretreatment of target area was used, through the Canny egde-detection, edge closed and two connected domain de-noising operations, the background texture clutter was removed to determine the edge of target. Then, piecewise linear fitting on the target bottom edge was used and the curve fitting results would be taken as the waterline. Finally, the gray value statistics was calculated to get the brightest area as the position of engine compartment. The experimental results show that this method has stability testing results and good robustness. It can be applied to detect the aim point of IR warship target in different viewing directions. The algorithm provides an effective solution for the problem of automatic selection of tracking point in target tracking.