A stabilized semi-implicit scheme was designed in [3] to solve the Functionalized Cahn-Hilliard (CCH) equation, but there is a lack of theoretical analysis of the energy stability. In this paper, we generalize this scheme to solve the general FCH mass-conserving gradient flow (FCH-MCGF) equation and show the theoretical analysis results about the unique solvability and energy stability. We successfully prove that this scheme is uniquely solvable and energy stable in theory by rewriting the double-well potential function to satisfy the Lipschitz-type condition. The range of stabilization parameters is theoretically given as well. In addition, another similar energy stable scheme is proposed, which slightly widens the range of stabilization parameters in theory and has almost the same precision as the previous one. Both the detailed numerical procedure and the selection of stabilization parameters are presented. Finally, several numerical experiments are performed for the FCH-MCGF equation based on these schemes. Specially, the adaptive time step size is considered in the scheme for the simulations of the phase separation in 2D and 3D, since any time step size can be used according to our theoretical results. Numerical results show that these schemes are energy stable and the large time step size indeed can be used in computations. Moreover, by comprehensive comparisons of stability and accuracy among the stabilized semi-implicit scheme, the convex splitting scheme, and the fully implicit scheme, we conclude that the performance of the stabilized semi-implicit scheme is the best, and the convex splitting scheme performs better than the fully implicit scheme.