Root cause analysis (RCA) of complex systems is important for identify countermeasures. Fault tree analysis (FTA) is one of the most commonly used tools for RCA. However FTA provides less guidance to analysts. Therefore it is difficult for them to exhaustively identify possible causes, and analysis results strongly depend on their skills. Spacecraft systems are among the largest and most complex man-made systems and consequently require the application of systems engineering methods in their development processes. Spacecraft development is particularly difficult because spacecraft operate in a low gravity and high vacuum environment, which make realistic system level tests impossible on earth before launch. For this reason, it is common that design and manufacture are complementarily verified by analysis. However, insufficient verification often results in on-orbit nonconformance, leading to unexpected anomalies in mission operations. This study proposes the use of the Dual Vee Model developed in recent advances on strategic systems engineering methodology for identifying the root cause of such anomalies. The proposed method facilitates exhaustive identification of possible causes. The usefulness of this approach has been demonstrated in the ADEOS-II spacecraft which is a three-ton class Japanese Earth-observing satellite. The Dual Vee Model consisting of the Architecture Vee and the Entity Vee is helpful in identifying the configuration items and the development sequence for determining the process that could have caused an anomaly.