A method for adaptively adjusting state transition time in a Peripheral Component Interconnect (PCI) Express (PCIe) system and associated apparatus such as a root complex (RC) device and an endpoint device are provided. The method may include: toggling a clock request signal on a signal path coupled between the RC device and the endpoint device based on a request from the RC device or on a request from the endpoint device, wherein when the clock request signal toggles, the endpoint device transits from a first state to a second state; and toggling a reference clock signal from the RC device at a timing determined according to a training parameter among at least one predetermined parameter which is set dependent on at least one of the factors: a transition time, a restoration delay, a latency tolerance report (LTR) and a bias state, after the clock request signal toggles.