The application of nitrogen fertilizer is crucial to the growth and biological nitrogen fixation of peanut, especially in the seedling stage where nodules have not yet formed. However, it is still uncertain how much initial nitrogen fertilizer should be applied to promote peanut root growth, nodule formation, and biological nitrogen fixation (BNF). There, a 2-year pot experiment was conducted using Huayu 22 (HY22, large-grain cultivar) and Huayu 39 (HY39, small-grain cultivar) as experimental materials to research the effects of different initial nitrogen fertilizer application rates on peanut root growth (root weight, root length, root mean diameter, root activity) and biological nitrogen fixation capacity (nodule number, nodule weight, biological nitrogen fixation, and nitrogen fixation potential per plant). N0, as control, four initial nitrogen fertilizer application rates were established: 15 kg·hm−2 (N15), 30 kg·hm−2 (N30), 45 kg·hm−2 (N45), and 60 kg·hm−2 (N60). The present results showed that the nodule number, nodule dry weight, nitrogenase activity, and biological nitrogen fixation of the HY22 cultivar under the N15 treatment were higher compared to those under other treatments over the two growing seasons. In addition, the cultivar of HY39 treated with the N15 treatment also increased the nitrogen fixation potential per plant and BNF relative to other treatments. Although the application of 60 kg·hm−2 nitrogen increased the root surface area and root volume, it decreased the nitrogenase activity, nodule dry weight, and nitrogen fixation potential per plant of HY22 and HY39 varieties in both growing seasons. Above all, an initial nitrogen application of 15 kg·hm−2 may be the optimal treatment for promoting peanut nodule formation and biological nitrogen fixation.