The addition of functional bacteria (FB) is low-cost and is widely applied in saline–alkali soil remediation, which may gradually become ineffective due to inter-specific competition with indigenous bacteria. To improve the adaptability of FB, the target FB strains were isolated from local saline–alkali soil, and the combined effects of FB and biochar were explored. The results showed that FB isolated from local soil showed better growth than the purchased strains under high saline–alkali conditions. However, the indigenous community still weakened the function of added FB. Biochar addition provided a specific niche and increased the relative abundance of FB, especially for Proteobacteria and Bacteroidota. As a result, the co-addition of 10% biochar and FB significantly increased the soil available phosphorus (AP) by 74.85% and available nitrogen (AN) by 114.53%. Zea Mays’s growth (in terms of height) was enhanced by 87.92% due to the decreased salinity stress and extra nutrients provided.