In this paper, we propose and analyze two stabilized mixed finite element methods for the dual-porosity-Stokes model, which couples the free flow region and microfracture-matrix system through four interface conditions on an interface. The first stabilized mixed finite element method is a coupled method in the traditional format. Based on the idea of partitioned time stepping, the four interface conditions, and the mass exchange terms in the dual-porosity model, the second stabilized mixed finite element method is decoupled in two levels and allows a noniterative splitting of the coupled problem into three subproblems. Due to their superior conservation properties and convenience of the computation of flux, mixed finite element methods have been widely developed for different types of subsurface flow problems in porous media. For the mixed finite element methods developed in this article, no Lagrange multiplier is used, but an interface stabilization term with a penalty parameter is added in the temporal discretization. This stabilization term ensures the numerical stability of both the coupled and decoupled schemes. The stability and the convergence analysis are carried out for both the coupled and decoupled schemes. Three numerical experiments are provided to demonstrate the accuracy, efficiency, and applicability of the proposed methods. KEYWORDS decoupled numerical methods, dual-porosity-Stokes model, horizontal wellbore, mixed finite elements, stabilization Int J Numer Methods Eng. 2019;120:803-833. wileyonlinelibrary.com/journal/nme 804 AL MAHBUB ET AL.model, It is not surprising that a great deal of effort has been devoted to develop appropriate numerical methods to solve the (Navier-)Stokes-Darcy fluid flow system, including coupled finite element methods, 17-21 domain decomposition methods, 22-31 Lagrange multiplier methods, 3,32,33 mortar finite element methods, 34,35 least-square methods, 36-38 partitioned time-stepping methods, 39,40 two-grid and multigrid methods, 41-44 discontinuous Galerkin finite element methods, 45-50 boundary integral methods, 51,52 and many others. [53][54][55][56][57][58] Although the traditional Stokes-Darcy model has been well studied, it has limitation to describe the heterogeneity of the porous medium which contains multiple porosities. It is worth to notice that the realistic naturally fractured reservoir consists of two coexisting and interacting medium, namely, tight matrix and microfractures. Furthermore, it is more important to characterize the intrinsic properties and accurately modeled the flow interactions between each medium. 59,60 The first multiporosity model was proposed by Barenblatt et al 61 for the naturally fractured reservoir in 1960 where the microfracture and matrix systems are formulated by individual but overlapping continua. Warren and Root 62 developed a homogeneous orthotropic dual-porosity model in 1963 based on the model proposed by Barenblatt. There are many applications for the dual-porosity model such as the geothermal system, hydrogeology, pe...