Abstract Background Heterogeneity of oil-bearing formations is one of major contributors to low oil recovery efficiency globally. Long-term water flooding will aggravate this heterogeneity by resulting in many large channels during the exploitation process. Thus, injected water quickly flows through these large channels rather than oil-bearing areas, which ultimately leads to low oil recovery. This problem can be solved by profile control using polymer plugging. However, non-deep profile control caused by premature plugging is the main challenge. Here, a conditional bacterial cellulose-producing strain, namely Enterobacter sp. FY-0701, was constructed for deep profile control to solve the problem of premature plugging. Its deep profile control and oil displacement capabilities were subsequently identified and assessed. Results The conditional bacterial cellulose-producing strain Enterobacter sp. FY-0701 was constructed by knocking out a copy of fructose-1, 6-bisphosphatase (FBP) encoding gene in Enterobacter sp. FY-07. Scanning electron microscope observation showed this strain produced bacterial cellulose using glucose rather than glycerol as the sole carbon source. Bacterial concentration and cellulose production at different locations in core experiments indicated that the plugging position of FY-0701 was deeper than that of FY-07. Moreover, enhanced oil recovery by FY-0701 was 12.09%, being 3.86% higher than that by FY-07 in the subsequent water flooding process. Conclusions To our knowledge, this is the first report of conditional biopolymer-producing strains used in microbial enhance oil recovery (MEOR). Our results demonstrated that the conditional bacterial cellulose-producing strain can in situ produce biopolymer far from injection wells and plugs large channels, which increased the sweep volume of injection water and enhance oil recovery. The construction of this strain provides an alternative strategy for using biopolymers in MEOR.