Permanent magnetic thick films are increasingly used in Micro-Electro-Mechanical Systems (MEMS) devices, but the interplay between magnetic properties, microstructure, and film thickness remains underexplored. We deposited SmCo-based films with thicknesses ranging from 350 nm to 1300 nm using magnetron sputtering at room temperature, followed by in-situ annealing. Our study examined the evolution of microstructure, phase composition, magnetic properties, and domain structures as thickness increases. The films displayed dense, fibrous structures typical of the zone T-type region, with 3D morphologies forming a network structure and an arc-shaped surface that expands with thickness. At thinner levels (around 350 nm), an amorphous SmCo phase predominates, prone to oxidation, while at greater thicknesses, the SmCo5 phase dominates but maintains a grain size of 12–15 nm. Coercivity decreases significantly from 33 kOe to 8 kOe as thickness increases from 630 to 1300 nm due to the diminishing pinning effect and dominance of the reversal domain nucleation mechanism. Analysis using magnetic force microscopy and micromagnetic simulations indicates that this reduction in coercivity is mainly due to the decomposition of the SmCo5 phase and a reduction in magnetic domain size.