It is very difficult to detect ballistic missiles because of small cross-sections of the radar and the high maneuverability of the missiles. In addition, it is very difficult to recognize and intercept warheads because of the existence of debris and decoy with similar motion parameters in each flight phase. Therefore, feature vectors based on the maneuver, the micro-motion according to flight phase are needed, and the two types of features must be fused for the efficient recognition of ballistic warhead regardless of the flight phase. In this paper, we introduce feature vectors appropriate for each flight phase and an effective method to fuse them at the feature vector-level and classifier-level. According to the classification simulations using the radar signals predicted by the CAD models, the closer the warhead was to the final destination, the more improved was the classification performance. This was achieved by the classifier-level fusion, regardless of the flight phase in a noisy environment.