In this work, we present an efficient way to decouple the multicontinuum problems. To construct decoupled schemes, we propose Implicit-Explicit time approximation in general form and study them for the fine-scale and coarse-scale space approximations. We use a finite-volume method for fine-scale approximation, and the nonlocal multicontinuum (NLMC) method is used to construct a coarse-scale approximation. The NLMC method is a multiscale method for developing an accurate and physically meaningful coarse-scale model based on defining the macroscale variables. The multiscale basis functions are constructed in local domains by solving constraint energy minimization problems and projecting the system to the coarse grid. The resulting basis functions have exponential decay properties and lead to the accurate approximation on a coarse grid. We construct a fully Implicit time approximation for semi-discrete systems arising after fine-scale and coarse-scale space approximations. We investigate the stability of the two and three-level schemes for fully Implicit and Implicit-Explicit time approximations schemes for multicontinuum problems in fractured porous media. We show that combining the decoupling technique with multiscale approximation leads to developing an accurate and efficient solver for multicontinuum problems.