This paper focuses on the parameter estimation issues of multivariate equation-error autoregressive moving average systems. By applying the gradient search and the multi-innovation theory, we derive a multi-innovation gradient based iterative (MI-GI) algorithm. In order to improve the computational efficiency and the parameter estimation accuracy, a filtering and decomposition based gradient iterative (F-D-GI) algorithm is presented by using the data filtering technique and the decomposition technique. The key is to choose an appropriate filter to filter the input-output data and to transform an original system into several subsystems. Compared with the MI-GI algorithm, the F-D-GI algorithm can generate more accurate parameter estimates. Finally, an illustrative example is provided to indicate the effectiveness of the proposed algorithms.