The development of plant-growth-promoting bacteria (PGPB) is one of the important research topics in agricultural microbiology. Four bacterial isolates that exhibited nitrogen fixation, phosphate and potassium solubilization, as well as indole-3-acetic acid (IAA) and siderophore production abilities, were selected from biogas residue, namely BR-1, BR-16, BR-17, and BR-44. According to morphological and molecular biological identification, BR-1, BR-16, BR-17, and BR-44 belonged to Bacillus subtilis, Bacillus cereus, Bacillus megaterium, and Bacillus subtilis, respectively. The four functional strains were combined into a composite microbial community. The optimal media were peptone (15 g/L), sucrose (10 g/L), and KCl (2 g/L); the optimal incubation conditions were an initial pH of 7.0, a volume of 47 mL/250 mL, an inoculum size of 6% v/v, an incubation temperature of 31 °C, a shaking speed of 205 r/min, and an incubation period of 20 h, as determined through a single factor test and the response surface methodology (RSM). In the optimized process, a liquid bacterial inoculant with an OD₆₀₀ of 1.866 was obtained, with an effective viable count of 8.955 × 10⁹ CFU/mL. A solid bacterial inoculant was prepared by using bran as a substrate, and its effective viable count was 1.11 × 10⁹ CFU/g. The application of the bacterial inoculants promoted the growth of watermelon, increased the photosynthetic efficiency and yield, and improved fruit quality. This study provides a theoretical basis and technical support for the development and application of microbial inoculants.