There are three deep faults in the aeromagnetic map of the Western Tianshan Mountains. These deep faults have very significant magnetic anomalies. They are not only the divisions of different tectonic units but also the important ore-controlling structure zones. In this paper, the authors deal with magnetic characteristics of the deep faults and the relationship between the deep faults and the mineralization. Nileke deep fault is one of the most important faults in this area. There are four large-size known iron ore deposits around Nileke deep fault. According to the latest high precision aeromagnetic survey, four anomalies have been proved to be related to the iron ore deposit. These anomalies are also located near Nileke deep fault.