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The extreme post-thermal environment of extra-heavy oil reservoirs, characterized by high salinity, anaerobiosis, and nutrient depletion, severely limits the efficacy of conventional Microbial Enhanced Oil Recovery (MEOR). To address this, a mild-thermal-assisted MEOR (MT-MEOR) strategy is proposed, which strategically leverages these reservoir adversities as selective pressures. The central hypothesis posits that such conditions can induce a beneficial phenotypic shift in specific microorganisms, transforming them into deep-delivery conformance control agents. The methodology integrates stress-responsive microbiological analysis with multiscale physical simulation. Laboratory studies demonstrate that under simulated reservoir stresses, Geobacillus WJ-8 undergoes a Spo0A∼P-regulated phenotypic shift from motility to cellular filamentation and copious extracellular polymeric substance (EPS) biosynthesis. This transition enables microbes to function as structural scaffolds and biological adhesives, autonomously constructing a three-dimensional, heterogeneous bioflocculation system in porous media via mechanisms including sweep flocculation and adsorption bridging. The key findings are as follows: (1) The core mechanism involves an environmentally triggered, self-responsive microbial flocculation process, presenting a novel strategy for MEOR. (2) The resulting compliant bioflocs effectively restrict flow in high-permeability zones, extending the operational permeability threshold for microbial conformance control to 2500–3000 mD without inducing formation damage. (3) Mild thermal activation at 70 °C is established as a critical factor for enabling macroscopic profile modification, achieving a 70% fractional flow contribution from the low-permeability zone and a 13.9% incremental oil recovery. (4) The system generates in situ biomass exceeding injected volumes via subsequent crude oil metabolism, establishing a self-reinforcing recovery mechanism. This research establishes a recovery paradigm where reservoir adversities are converted into biochemical drivers via an autonomous, stress-responsive microbial system. The findings advance the potential of microbial processes to unlock ultraheavy oil reserves.