Electro-hydraulic systems are extensively utilized to generate desired acceleration waveforms to provide a vibration environment for testing the performance and reliability of objects in various industrial applications. However, as electro-hydraulic systems are often affected by some inevitable drawbacks resulted from hydraulic nonlinearities, unwanted dynamic variations and disturbances, the generated acceleration waveform is generally far behind the expectation. In this paper, a convex combined adaptive controller with input shaping technique is proposed for enhancing the transient acceleration waveform replication accuracy of electro-hydraulic systems. The proposed controller is comprised of a three variable controller at the bottom level, an input shaping technique controller at the middle level, and a convex combined adaptive controller at the upper level. The three variable controller is firstly utilized for the establishment of a fundamental closed-loop acceleration control system, and then the input shaping technique controller is constructed by introducing an offline designed inverse prefilter utilizing the multi-innovation recursive least squares algorithm and the zero magnitude error tracking algorithm. The convex combined adaptive controller at the upper level is comprised of two individual adaptive filters with high and low step sizes, which provides the merits of fast convergence rate and high tracking accuracy, and it is further exploited to address for system’s dynamic variations, model uncertainties and unexpected perturbations. Comparative experiments of the proposed controller with a manually generated random waveform and a recorded earthquake waveform as the testing inputs are conducted on a typical electro-hydraulic test bench, and the corresponding results demonstrate the feasibility and superiority of the proposed controller in improving the transient acceleration waveform replication performance of electro-hydraulic systems.