Abstract: The intermediate channel between two decentralized cascade locks is an impounded navigation channel. The filling and emptying of lock chambers during lock operation leads to oscillations of the free-surface elevation in the channel, which can increase the degree of difficulty encountered in maneuvering a ship and even produce ship accidents in some instances. In previous works, most of the research effort has been devoted to the propagation of long waves in intermediate navigation channels. In contrast, the study of secondary waves in the channels has received less attention so far. In the present study, the development of secondary waves under the layout of decentralized cascade locks for the new waterway in the Three Gorges project was fully considered. A coupled model based on the basic equations of ship locking and Boussinesq equations was first established. Subsequently, the development length of secondary waves and its response to related hydraulic parameters were investigated. The results demonstrated that during lock emptying, the development length of secondary waves was solely related to the maximum discharge per unit width in a form of power function. In contrast, the relationship between the development length and the maximum discharge per unit width was not unique but depended on the initial head of lock chambers during lock filling. Based on the numerical results, two empirical formulas were proposed to predict the development length under different locking operations. The present finding can provide theoretical guidance and technical support for the hydraulic design and operation of decentralized cascade locks.