Uncontrolled flow through different permeability zones in oil reservoirs remains a huge challenge during water flooding, which can significantly limit microbial-enhanced oil recovery (MEOR)) efficiency. The aim of the present work was to use polymer-based plugging to assist MEOR through laboratory simulation and field tests. An indigenous strain HB3 was evaluated under field-relevant conditions. A polymeric HPAM/Cr(III) plugging system was optimized which was also compatible with the microorganism. Laboratory-based simulation demonstrated the selective plugging with HPAM/Cr(III) resulting in enhanced oil recovery more significantly in the low-permeability core, increasing from 12.8% to 47.5%, compared to that in the high-permeability one, from 47.1% to 63.2%. A subsequent microbial injection enhanced the oil recovery further, also with more effective enhancement in the low-permeability core, increasing from 49.5% to 70.0% while from 67.5% to 78.0% in the high permeability one. The field tests involving two water injection and nine oil production wells confirmed the improvement of deep profile control by polymer-based plugging, resulting in a more uniform distribution of water absorption. With subsequent microbial injection, oil recovery was significantly enhanced, achieving an ultimate recovery of 57.6% and a cumulative oil increment of 3486 t in nine wells over the 7 month field tests. It was demonstrated that the application of polymer-based plugging significantly improved MEOR efficiency, providing a new route for EOR, especially for heterogeneous reservoirs.