Helicopter fuselage vibration is mainly caused by rotor excitation loads. Active vibration control (AVC) has become an effective means to reduce helicopter fuselage vibration. The higher harmonic control (HHC) algorithm in the frequency domain has been widely used in AVC due to advantages such as simplicity, strong robustness, and ease of implementation. However, HHC has drawbacks such as long updating intervals of control inputs and updating delays. The harmonic synchronous identification-updating (HSIU) algorithm can effectively address the drawbacks of HHC, but its convergence speed depends on the updating step size. These frequency domain algorithms can effectively suppress the steady-state vibration responses of the fuselage, but the AVC effect is significantly decreased when the rotor excitation loads are strongly time-varying. In this paper, a fluctuating harmonic control (FHC) algorithm is proposed to achieve fast convergence and high effectiveness for the AVC of a helicopter fuselage under strongly time-varying loads. AVC simulations of a helicopter fuselage structure under several strongly time-varying loads were conducted by using the HHC, HSIU, and FHC algorithms, respectively, indicating that the FHC algorithm proposed in this paper can efficiently and quickly control helicopter fuselage vibration under strongly time-varying loads.