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This paper is concerned with a blood flow problem coupled with a slow plaque growth at the artery wall. In the model, the micro (fast) system is the Navier-Stokes equation with a periodically applied force and the macro (slow) system is a fractional reaction equation, which is used to describe the plaque growth with memory effect. We construct an auxiliary temporal periodic problem and an effective time-average equation to approximate the original problem and analyze the approximation error of the corresponding linearized PDE (Stokes) system, where the simple front-tracking technique is used to update the slow moving boundary. An effective multiscale method is then designed based on the approximate problem and the front tracking framework. We also present a temporal finite difference scheme with a spatial continuous finite element method and analyze its temporal discrete error. Furthermore, a fast iterative procedure is designed to find the initial value of the temporal periodic problem and its convergence is analyzed as well. Our designed front-tracking framework and the iterative procedure for solving the temporal periodic problem make it easy to implement the multiscale method on existing PDE solving software. The numerical method is implemented by a combination of the finite element platform COMSOL Multiphysics and the mainstream software MATLAB, which significantly reduce the programming effort and easily handle the fluid-structure interaction, especially moving boundaries with more complex geometries. We present some numerical examples of ODEs and 2-D Navier-Stokes system to demonstrate the effectiveness of the multiscale method. Finally, we have a numerical experiment on the plaque growth problem and discuss the physical implication of the fractional order parameter.