The safety and reliability of wind turbines subjected to multiple loads has recently attracted great attention. To investigate how soil-structure interaction (SSI) affects the seismic performance of operating wind turbines, a wind tunnel-shaking table test platform has been built which can realize applying wind load and seismic load simultaneously. A 1:100-scaled wind turbine model with two different kinds of foundations (soil-structure interactive foundation and rigid foundation) has been tested under four seismic excitations (El-Centro and Taft, input in two directions) when it keeps operating in wind excitations. Nacelle displacement with the soil-structure interactive foundation was significantly larger than that of the rigid foundation, reaching 3–5 times at a peak ground acceleration (PGA) of 0.8 g. The maximum nacelle displacement of the scaled model with soil-structure interactive foundation always occurs in the direction of incoming wind, unlike the rigid one occurring in the direction of seismic input direction. The rigid foundation model presents a strong whipping effect with an acceleration amplification factor of the tower top (APF = 3). In contrast, the model with soil-structure interactive foundation shows mild whipping effect due to smaller foundation stiffness (APF of the tower top = 1.5). The study demonstrates SSI could weaken dynamic responses, reducing bending moments but inducing excessive nacelle displacement, risking structural damage. This study underscores the importance of SSI in evaluating the safety and reliability of wind turbines subjected to the wind and seismic loads and provides experimental results for future designs. •A joint wind tunnel and shaking table test system is developed for testing scaled wind turbine in operation.•Various soil-structure interactions, wind loads, seismic loads and operation loads are considered in the tests.•Dynamic characteristics and displacement, acceleration and bending moment are measured and analysed.•Compared to rigid foundation, soil-structure interaction leads to greater displacement but less acceleration and bending moment.