Understanding the response of performance of two-stage turbine to pulsating flow in exhaust manifold system is essential for performance improvement of engine. This paper studies unsteady interaction of two turbines in a two-stage turbocharging system via experimental method and a reduced order model. Firstly, experimental results of the unsteady pressure ratio of two turbines are discussed in cases with different engine speeds, engine loads, and bypass valve openings. Results show that the pressure ratio distribution between two turbines is profoundly influenced by the engine condition. The pressure ratio of low-pressure turbine (LPT) increases consistently with the engine speed and load, while it increases slightly or even remains unchanged for high-pressure turbine (HPT). HPT is de-loaded when the bypass valve is open, and there are large numbers of fluctuations with high frequencies in the trace of pressure ratio when the bypass valve is open. Next, a reduced order model of the two-stage turbine is established for turbine responses at pulsating conditions, and model validations of performance and unsteady pressure in two-stage turbine all show high precision. Finally, the model is applied for performance analysis of two-stage turbine system under pulsating conditions. The results show that with the increase in engine speed, load or bypass valve opening, the hysteresis loops of both turbines are expanded around the steady performance curve. However, the deviation of cycle-average performance from steady case for two turbines is notably different. LPT shows a stronger throttling effect at pulsating inflows. Moreover, compared with steady performance for whole two-stage turbine, cycle-average performance is reduced for all pulsating cases, especially for cases of open valve. The differences in turbine performance of two-stage turbine system caused by gasdynamic coupling effect of two turbines are suggested to be considered in the turbo-engine matching.