The yield and the equivalence factor are key parameters of the ecological footprint model. It is significant to evaluate the values' uncertainties to improve the ecological footprint model. Using the Niulanjiang Watershed as a case study, this study assessed the ecological footprint and capacity of the whole watershed and its 11 counties separately through the ecological footprint model. The local yield factor was calculated and compared with the most-often used values from around the world to estimate the uncertainty of the model. The results showed that the ecological footprint of the Niulanjiang Watershed is 3521404 ghm², and the biological capacity is 2338535 ghm², indicating unsustainability. Guandu County occupies the largest ecological overshoot among the counties in the watershed. The equivalence and yield factors vary greatly in different studies. The maximum equivalence factor of cropland was 4.16 times that of the minimum, and the maximum yield factor of grassland was 4.16 times that of the minimum. The estimated ecological footprint, capacity, and overshoot using the maximum equivalence and yield factor were 2.5 times, 3.9 times, and 1.4 times those using the minimum respectively. Due to its special climate and topography, and the low level of development of animal husbandry and fisheries, the ecological footprint of Niulanjiang Watershed needs to be classified in detail; global and national factors cannot be applied directly.