The seeds of quinoa variety “Yilong No.1” were used as experimental material in pot in 2016. We studied the effects of inoculating two kinds of arbuscular mycorrhizal fungi (AM) including Glomus mosseae (Gm) and Glomus tortuosum (Gt) on the quinoa growth, root growth indicators and root physiological indicators under the different nitrogen application rates of 0, 0.2, 0.4 and 0.6 g/kg, to provide the theoretical basis for increasing the utilization rate of nitrogen fertilizer and improve the growth of quinoa. The main results showed that: (1) inoculation of Glomus mosseae had the highest infection rate and mycorrhizal dependency of quinoa under 0.4 g/kg nitrogen application rate. (2) Under the same inoculated treatment, plant height, stem diameter, leaf area, aboveground weight, total root length and other root growth indicators, antioxidant enzyme activities of root system of quinoa seeds were initially increased and then decreased with the increasing nitrogen application rate; compared with the uninoculated treatment, the above indicators were significantly improved after AM fungi was inoculated. The values reached the maximum in the 0.4 g/kg nitrogen application rate, and the increase of Gm was greater than that of Gt. (3) Under the same inoculated treatment, MDA content, soluble sugar content and proline content were initially decreased and then increased with the increasing nitrogen application rate; compared with the uninoculated treatment, the MDA content was significantly reduced after AM fungi was inoculated, soluble sugar content and proline content were significantly increased after AM fungi was inoculated. Meanwhile, after inoculating Gm the decrease of MDA content, the increase of soluble sugar content and proline content were greater than that of incoculating Gt. These results showed that the infection rate and mycorrhizal dependency in root of quinoa with the proper nitrogen application rate increasing, the growth of aboveground and root of quinoa were promoted, meanwhile, increased the accumulation of antioxidant enzymes and osmotic adjustment substances, decreased the accumulation of harmful substances, especially 0.4 g/kg nitrogen application rate and Glomus mosseae were favorable for quinoa seeds to increase growth.