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Abstract Mass-conserved reaction-diffusion systems are used as mathematical models for various phenomena such as cell polarity. Numerical simulations of this system present transient dynamics in which multiple stripe patterns converge to spatially monotonic patterns. Previous studies indicated that the transient dynamics are driven by a mass conservation law and by variations in the amount of substance contained in each pattern, which we refer to as “pattern flux”. However, it is challenging to mathematically investigate these pattern dynamics. In this study, we introduce a reaction-diffusion compartment model to investigate the pattern dynamics in view of the conservation law and the pattern flux. This model is defined on multiple intervals (compartments), and diffusive couplings are imposed on each boundary of the compartments. Corresponding to the transient dynamics in the original system, we consider the dynamics around stripe patterns in the compartment model. We derive ordinary differential equations describing the pattern dynamics of the compartment model and analyze the existence and stability of equilibria for the reduced ODE with respect to the boundary parameters. For a specific parameter setting, we obtained results consistent with previous studies. Moreover, we present that the stripe patterns in the compartment model are potentially stabilized by changing the parameter, which is not observed in the original system. We expect that the methodology developed in this paper is extendable to various directions, such as membrane-induced pattern control.