This paper presents a virtual dynamic vibration absorber (DVA) trap fusion active vibration suppression algorithm based on inertial actuators as a solution to the harmonic vibration control problem of large flexible space trusses. Firstly, the mechanism of the inertial actuator is analyzed, and the relationship between the bandwidth of the algorithm and the intrinsic frequency of the inertial actuator is derived. Secondly, a dynamic model of the space truss is constructed. Subsequently, an analysis is conducted to determine the manner in which the virtual DVA exerts influence on the system’s dynamic characteristics. Based on this analysis, a virtual DVA trap fusion active vibration suppression algorithm is designed. Finally, the efficacy of the proposed algorithm in suppressing vibration is demonstrated through experimentation. The algorithm was demonstrated to be effective in suppressing both single-frequency harmonic vibration and multi-frequency harmonic vibration under the working conditions of single-degree-of-freedom and multi-degree-of-freedom of a flexible truss. The vibration suppression efficiency was found to be greater than 60%. It is therefore evident that the proposed algorithm has the potential to be applied to the vibration suppression of telescopes assembled in orbit in the future.