Complex disturbances with multifrequency components inevitably exist in the attitude control system of flexible spacecrafts. Multirate iterative learning disturbance observer (MILDO) is a promising solution to estimate and attenuate these disturbances much more accurately. However, measurement delay in the attitude measurement system may severely degrade the estimation performance of MILDO and even lead to instability of the control system. To suppress complex disturbances of flexible spacecrafts subject to a known measurement delay, a delay compensation-MILDO (DC-MILDO) is proposed in this study. First, an augmented model is constructed for the delayed disturbance by introducing slowly varying disturbance, multiple periodic disturbances, and the integral of the lumped disturbance as states. Then, a virtual measurement of the system is built by realigning the control torques with the delayed measurements in spacecraft attitude dynamics. According to the augmented model and the virtual measurement, a modified MILDO is designed by using multiple iterative learning structures. Based on the estimates of the modified MILDO, the lumped disturbance at current instant can be predicted by compensating time delay in the multifrequency components. Subsequently, a composite controller for flexible spacecraft is built by combining DC-MILDO with a robust controller based on Lyapunov–Krasovskii approach. Simulation results demonstrate the effectiveness of the proposed controller.