An apparatus and method for adaptively changing clock frequencies of a Central Processing Unit (CPU) and a bus in a digital system are provided. The system includes an Adaptive Frequency Scaling (AFS) controller and a clock controller. The AFS controller determines whether to change a clock frequency of the CPU according to operation information of the CPU, and determines whether to change a clock frequency of the bus according to operation information of the bus. The clock controller generates a clock frequency of the CPU and a clock frequency of the bus according to the determination of the AFS controller.