With the rapid development of ecological agriculture and organic products, there is an urgent need to reduce the use of fertilizers and pesticides by producing bio-nursery substrates containing multifunctional microbial communities. In this study, beneficial Pseudomonas strains were screened from the rhizosphere of muskmelon (Cucumis melo L.) pre-inoculated with Bacillus velezensis R1-3. The ability of the strain to dissolve phosphorus and produce indole-3-acetic acid (IAA), the effect of the strain on seed germination rate, and the antagonism with R1-3 were determined. Four strains of beneficial Pseudomonas strains that had no antagonistic effect against R1-3 were obtained and formed a Bacillus–Pseudomonas community. The seedling effect of biological substrates containing the Bacillus–Pseudomonas community was evaluated using a seedling pot experiment and a pot experiment. The results showed that the phosphorus solubilization range of all Pseudomonas strains was 86.32–459.48 mg L−1 and the IAA production range was 2.98–11.86 mg L−1. There was a significant negative correlation between the amount of phosphorus dissolved in the fermentation solution and pH. Combined with the results of the seed germination rate and antagonism test, the strains R1-3 + HY-S7, R1-3 + HY-S25, R1-3 + HY-S36, and R1-3 + HY-S70 were selected for the seedling pot experiment and the pot experiment. The results of the two-season seedling culture and two-season pot experiments showed that the bio-nursery substrates containing the bacterial community R1-3 + HY-S70 significantly promoted the growth of muskmelon seedlings, improved plant height, maximum leaf length, and fresh weight, and were significantly better than single bacterial and control treatments at increasing plant height and fresh weight. Finally, the bacterial community R1-3 + HY-S70 was established as the optimal combination for developing biological seedling substrates. Based on 16S rDNA gene sequence analysis, the strain HY-S70 was preliminarily identified as Pseudomonas moraviensis.