The flow-induced flutter has a significant role in aircraft stability, renewable energy extraction, animal locomotion, among many other applications. While being a ubiquitous phenomenon, the control of the flutter response has been primarily limited to simplified systems and, often, with the help of linear inviscid flow theories. In this paper, we numerically investigate how the plunging response of a foil can be regulated using an active flap to improve structural safety or enhance the energy extraction efficiency of the foil with a tightly coupled fluid-structure interaction algorithm. A broad range of foil and flap settings was tested and their flow dynamics have been investigated. A novel multi-scale modal analysis technique suitable for fluid-structure interaction systems successfully isolates the active flap-induced and the flow-induced modes. It is observed that the competition between these two modes dictates the plunging response of the foil. The active flap can modulate the leading edge vortex shedding with larger flapping amplitude and regulate the foil heaving motion. The ratio of the competing modal energy is proposed to evaluate the control efficacy of the morphing surface, and the onset of the lock-in is associated with the ratio approaching unity. It is shown that the morphing flap is a good candidate for active flow control.