In this paper, we propose and analyze a novel stabilized finite element method (FEM) for the system of generalized Stokes equations arising from the time-discretization of transient Stokes problem. The system involves a small viscosity, which is proportional to the inverse of large Reynolds number, and a large reaction coefficient, which is the inverse of small time step. The proposed stabilized FEM employs the $C^0$ piecewise linear elements for both velocity field and pressure on the same mesh and uses the residuals of the momentum equation and the divergence-free equation to define the stabilization terms. The stabilization parameters are fixed and element-independent, without a comparison of the viscosity, the reaction coefficient and the mesh size. Using the finite element solution of an auxiliary boundary value problem as the interpolating function for velocity and the $H^1$-seminorm projection for pressure, instead of the usual nodal interpolants, we derive error estimates for the stabilized finite element approximations to velocity and pressure in the $L^2$ and $H^1$ norms and most importantly, we explicitly establish the dependence of error bounds on the viscosity, the reaction coefficient and the mesh size. Our analysis reveals that this stabilized FEM is particularly suitable for the generalized Stokes system with a small viscosity and a large reaction coefficient, which has never been achieved before in the error analysis of other stabilization methods in the literature. We then numerically confirm the effectiveness of the proposed stabilized FEM. Comparisons made with other existing stabilization methods show that the newly proposed method can attain better accuracy and stability.