System identification provides many convenient and useful methods for engineering modeling. This paper targets the parameter identification problems for multivariable equation-error autoregressive moving average systems. To reduce the influence of the colored noises on the parameter estimation, the data filtering technique is adopted to filter the input and output data, and to transform the original system into a filtered system with white noises. Then we decompose the filtered system into several subsystems and develop a filtering based partially-coupled generalized extended stochastic gradient algorithm via the coupling concept. In contrast to the multivariable generalized extended stochastic gradient algorithm, the proposed algorithm can give more accurate parameter estimates. Finally, the effectiveness of the proposed algorithm is well demonstrated by simulation examples.