The invention discloses a functional biological fixation in-situ remediation method for underground water polluted by nitrogen, belonging to the field of underground water remediation. The method comprises the following steps of: preparing immobilized materials; separately gathering autotrophy denitrifying bacteria; immobilizing microbes; and carrying out embedding and running processing on an immobilized carrier in the well completion process. The immobilized materials are obtained by selecting an optimal carrier material to prepare an adsorbent, and the denitrifying microbes are gathered from a primitive environment, immobilized and then placed into the primitive environment, the bacteria is ensured to exist and propagate in a stratal environment and the reaction residence time is controlled by controlling the water yield of a pumping well, thereby achieving the optimal denitrifying effect; in addition, the invention has obvious demonstration effect on processing the nitrogen-pollution of the underground water and good processing effect and is suitable for being popularized to wide underground water regions polluted by nitrogen.