The invention provides a method for deeply treating micro-polluted source water through in-situ enrichment, immobilization and acclimatization of indigenous microorganisms. In-situ enrichment and immobilization of the indigenous microorganisms are carried out in a stuffy aeration manner under an appropriate aeration condition by inoculating underwater bed sediment to be treated and water to be treated and adding nutrient elements; then, the immobilized microorganisms are gradually adapted to the water quality to be treated by arranging automatic water intake/discharge, gradually reducing the concentration of the nutrient elements in intake water and increasing the amount of intake/discharged water. The method disclosed by the invention has the following advantages: 1) under the stuffy aeration condition, loss of the microorganisms is avoided, multiplication of the indigenous functional microorganisms is accelerated, and the start time of the process is greatly shortened; 2) the multiplication of autotrophic nitrobacteria flora is preferably promoted by inoculating the underwater bed sediment having nitrobacteria flora of high abundance, adding ammonia nitrogen and reducing a carbon nitrogen ratio, and the diversity of the inoculated nitrobacteria flora is ensured by inoculating the underwater bed sediment having an appropriate depth, and therefore the operation stability of a system is promoted.