In contrast to research on active sites in nanomaterials, lithium tantalate single crystals, known for their exceptional optical properties and long-range ordered lattice structure, present a promising avenue for in-depth exploration of photocatalytic reaction systems with fewer constraints imposed by surface chemistry. Typically, the isotropy of a specific facet provides a perfect support for studying heteroatom doping. Herein, this work delves into the intrinsic catalytic sites for photocatalytic nitrogen fixation in iron-doped lithium tantalate single crystals. The presence of iron not only modifies the electronic structure of lithium tantalate, improving its light absorption capacity, but also functions as an active site for the nitrogen adsorption and activation. The photocatalytic ammonia production rate of the iron-doped lithium tantalate in pure water is maximum 26.95 μg cm−2 h−1, which is three times higher than that of undoped lithium tantalate. The combination of first-principles simulations with in situ characterizations confirms that iron doping promotes the rate-determining step and changes the pathway of hydrogenation to associative alternating. This study provides a new perspective on in-depth investigation of intrinsic catalytic active sites in photocatalysis and other catalytic processes.