Maize/peanut intercropping is practiced widely to increase land productivity and considered a sustainable way for using and saving resources through peanut’s complementary N source via biological N2 fixation. Our study aims to understand how maize/peanut intercropping affects the nodulation of peanuts under water-limiting conditions and different nitrogen inputs. A two-year micro-plot experiment in 2015–2016 and a two-year field experiment in 2017–2018 were conducted to quantify nodulation in maize/peanut intercropping and sole peanut cropping under four N fertilization rates (N-free, low, medium, and high N) in rain-fed water-limited conditions. In the micro-plot experiment, intercropped peanuts increased nodule biomass compared to sole peanuts. The nodule number of intercropped peanuts was 51.6% (p = 0.001) higher than that of sole cropped peanuts, while nodule weights did not differ at high N fertilization rates and were lower in the no-N fertilization control. However, the results were different in the field experiment. Both the nodule number and single weight of the sole cropped peanut were 48.7% (p = 0.020) and 58.9% (p = 0.014) higher than that of the intercropped peanut. The ratio of the nodule weight to aboveground dry matter at the beginning peg in the dry year of 2017 was lower in intercropping than sole cropping, especially at low N fertilization rates. The potential increase in nodulation found in a well-controlled micro-plot environment might be limited by strong water and light competitions in field conditions. The results could contribute to the understanding of interspecific interactions in cereal/legume intercropping.