This study researches the tracking control problem for discrete-time systems with multiple input delays affected by sinusoidal disturbances. This study is organized around the expression of sinusoidal and disturbances and the delay-free transformation. First, based on the periodic characteristic of the sinusoidal disturbance, the sinusoidal disturbances are considered as the output of an exosystem. By proposing a discrete variable transformation, the discrete-time system with multiple input delays and the quadratic performance index are transformed into equivalent delay-free ones. Then, by constructing an augmented system that comprises the states of the exosystems of sinusoidal disturbances, the reference input, and the delay-free transformation systems, the original tracking problem is transformed into the optimal tracking problem for a delay-free system with respect to the simplified performance index. The optimal tracking control (OTC) law is obtained from Riccati and Stein equations. The existent and uniqueness of the optimal control law is proved. A reduced-order observer is constructed to solve the problem of physically realizable for the items of the reference input and sinusoidal disturbances. Finally, the feasibility and effectiveness of the proposed approaches are validated by numerical examples.