Abstract: The flowering and boll development stage is the key period for cotton yielding. Waterlogging during this stage inhibits cotton development and reduces final yield significantly. Nitrogen is considered to be an effective up-regulatory nutrient for crop growth. The objective of this investigation was to evaluate the effects of nitrogen fertilization on the gas exchange and chlorophyll fluorescence parameters under a short-term waterlogging for about eight days. Pot experiments were conducted with three N levels, namely N 0, 3.73 and 7.46 g/pot (equivalent to N 0, 240 and 480 kg/ha). The results show that chlorophyll and carotenoid contents and the Chl/Car ratio are significantly decreased under the waterlogging, and net photosynthetic rate (PN) and stomatal conductance (Gs) are reduced and the reduced degree of PN and Gs are increased with the increase of N application. The minimum fluorescence (Fo) and non-photochemical quenching coefficient (qN) are increased under the waterlogging, while the maximum photochemical efficiency of open photosystem (Fv/Fm), the quantum yield of electron transport (ΦPSⅡ) and the photochemical quenching (qP) are decreased. The increased degree of Fo and qN, and the reduced degree of Fv/Fm, ΦPSⅡ and qP are enhanced with the increase of N application. At the time of terminating the waterlogging, the PN, Gs, Fv/Fm, ΦPSⅡ and qP of the waterlogged cotton are decreased with the increase of N application, while the Fo and qN behave contrarily. Both biomass and seed cotton yield, which are affected by the waterlogging, are the highest under the N 240 kg/ha fertilization.