Poly-γ-glutamic acid (γ-PGA) is a natural polymer whose molecular weight and viscosity are critical for its application in various fields. However, research on super-high-molecular-weight or -viscosity γ-PGA is limited. In this study, the pgdS gene in Bacillus licheniformis WX-02 was knocked out using homologous recombination, and the batch fermentation performances of the recombinant strain WX-ΔpgdS were compared to those of WX-02. Nitrate accumulation was observed in the early fermentation stages of WX-ΔpgdS, and gene transcription analysis and cell morphology observations revealed that nitrite accumulation was caused by oxygen limitation due to cell aggregation. When the aeration and agitation rates were increased to 2.5 vvm and 600 r/min, respectively, and citrate was used as a precursor, nitrite accumulation was alleviated in WX-ΔpgdS fermentation broth, while γ-PGA yield and broth viscosity reached 17.3 g/L and 4988 mPa·s. Scanning electron microscopy (SEM) showed that the γ-PGA produced by WX-ΔpgdS exhibited a three-dimensional porous network structure. At a γ-PGA concentration of 5 mg/L, the fermentation broth of WX-ΔpgdS achieved a flocculation efficiency of 95.7% after 30 min of microalgae settling. These findings demonstrate that pgdS knockout results in super-high-viscosity γ-PGA, positioning it as an eco-friendly and cost-effective biocoagulant for microalgae harvesting.