Abstract: Polymer gels are widely used in water control and enhanced oil recovery in oil fields. However, the damage mechanism of polymer gels to layers with remaining oil and not requiring plugging and corresponding protective measures are unclear. In this paper, we investigated polymer gels' damage and protection performance through static gel-breaking experiments and dynamic plugging and oil recovery evaluations on rock cores. Moreover, nuclear magnetic resonance (NMR) technology was combined to analyze the damage performance of polymer gels on cores from the pore scale. In addition, a protective technique based on gel breakers for layers with remaining oil and not requiring plugging was proposed. Results showed that when polymer gels were injected into heterogeneous cores, they plugged high-permeability layers while also penetrating low-permeability layers. When the damage to the low-permeability layers was not alleviated, the conformance and oil displacement efficiency were significantly reduced. When the concentration of ammonium persulfate was 2%–5%, the gel-breaking time was shortest and the residue was very minimal. Therefore, ammonium persulfate could be used as a gel breaker and reservoir protective material. Furthermore, after injecting ammonium persulfate into heterogeneous reservoir cores, the gel damage on the face of low-permeability layers was relieved. Consequently, the improvement in sweep efficiency was achieved, showing the re-activation of the remaining oil in medium-low permeability layers. Therefore, the low-permeability layer protection process and core experiment study based on gel-breaking agents proposed in this study were suggested to provide a new technique for the field application of conformance modification agents, aiming to achieve higher recovery degrees.