Influenced by water injection, a dominant flow channel is easily formed in the high water cut stage of a conglomerate reservoir, resulting in the inefficient or ineffective circulation of the injected water. With gel flooding as one of the effective development methods to solve the above problems, its parameter optimization determines its final development effect, which still faces great challenges. A new optimization method for gel flooding is proposed in this paper. Firstly, the gel flooding parameters were obtained through physical experiments; then, an experimental model of gel flooding was established according to the target reservoir, and parameter sensitivity analysis was carried out. Next, a history matching of the gel flooding experiment was carried out. Finally, history matching of the target reservoir was also carried out, and a gel flooding scheme was designed and optimized to determine the best parameters. The experimental results showed that the gelation time was 4 h and the gel viscosity was 6332 mPa·s; the breakthrough pressure, resistance factor (RF), and residual resistance factor (RRF) all decreased with the increase in permeability. The gel had a good profile control ability and improved oil recovery by 16.40%. The numerical simulation results illustrated that the porosity of the high permeability layer (HPL) had the greatest impact on the cumulative oil production (COP) of the HPL, and the maximum polymer adsorption value of the HPL had the largest influence on the COP of the low permeability layer (LPL) and the water cut of both layers. Benefiting from parameter sensitivity analysis, history matching of the gel flooding experiment and a conglomerate reservoir in the Xinjiang A Oilfield with less time consumed and good quality was obtained. The optimization results of gel flooding during the high water cut stage in a conglomerate reservoir of the Xinjiang A Oilfield were as follows: the gel injection volume, injection rate, and polymer concentration were 2000 m3, 50 m3/d, and 2500 mg/L, respectively. It was predicted that the water cut would decrease by 6.90% and the oil recovery would increase by 2.44% in two years. This paper not only provides a more scientific and efficient optimization method for gel flooding in conglomerate reservoirs but also has important significance for improving the oil recovery of conglomerate reservoirs.