In this paper, we explore the consensus control scheme of stochastic perturbed nonlinear multi-agent systems with impulsive protocol and comparison system method. The effective variable impulsive consensus method is used to remove the restriction of fixed impulsive instants, which is more reliable and flexible in practical applications. From the theory of impulsive differential system, comparison system and stochastic differential system, some sufficient consensus conditions are derived and the relation between the system parameters and impulsive time window is analyzed extensively. The effectiveness of the proposed control method is confirmed by the numerical simulations finally.