We consider an unsteady micropolar fluid flow in a two-dimensional domain Ωε. The velocity field is assumed to satisfy a fluid-solid friction interface condition on a part of the boundary while the micro-rotation field satisfies non-homogeneous Dirichlet boundary conditions. The problem is thus described by a non-linear coupled variational parabolic system for the fluid velocity vϵ, the pressure pϵ and the angular micro-rotation field Zϵ. The thickness and the roughness of the fluid domain are described by multiple separated scales of periodic oscillations, i.e. Ωε={(z1,z2):0<z1<L,0<z2<εmhε(z1)} with hε(z1)=h(z1,z1ε,z1ε2,⋯,z1εm), 0<ε<<1, and m≥2. Existence, uniqueness and uniform estimates of the solution (vϵ,pϵ,Zϵ) are stated. Then we study the asymptotic behaviour of the flow as ε tends to zero by using the multiple scale convergence method for reiterated homogenization. The assumption m≥2 raises several technical difficulties in the limit process and leads to non-standard divergence free conditions for the limit velocity. We derive the limit problem which is totally decoupled for the limit velocity and pressure (v0,p0) on the one hand and the limit micro-rotation field Z0 on the other hand. More precisely (v0,p0) is solution of a variational elliptic inequality and Z0 solves an elliptic partial differential equation, where the time variable appears as a parameter. Moreover we prove that v0,p0 and Z0 are uniquely determined by auxiliary well-posed problems.