Many invasive plants are highly tolerant of disturbances and can invade various habitats, leading to difficulties in managing them. Most of control techniques need to be performed repeatedly, and the efficiency of the same control method may vary along environmental gradients. To develop a control strategy for an invasive plant in heterogeneous environments, it is important not only to optimize the control regime, but also to consider the efficiency in different habitats. We conducted a field experiment to test ow clipping regime (i.e., initial treatment timing and treatment interval) and habitat type (i.e., high and low tidal zones) influence the control efficiency for invasive Spartina alterniflora in an estuarine salt marsh. Among the 12 treatments, double-clipping treatment performed in early July and mid September (9- week-interval) had the highest efficiency, which not only eliminated sexual reproduction of S. alterniflora, but also inhibited its vegetative growth in the current and following years. The clipping efficiency in low tidal zonewas higher than that in high tidal zone. Therefore, an optimized control strategy for the invasive plants could be established based on the efficient control regime and habitat types. According to our study, a recommended double-clipping control strategy for S. alterniflora is that the initial clipping treatment is performed in the flowering period and the second one is performed 9 weeks later. In order to effectively reduce proliferation of the invasive plant, we suggest that the clipping regime should be applied for at least 2–3 years in low tidal zone and 3–4 years in high tidal zone.