Abstract: Abstract：This study aimed to investigate the influence of the waterlogging on the photosynthesisof the cotton using ahyperspectral model based on the photochemical reflectance index (PRI) and fluorescence ratio index (FRI). A fieldexperiment was performed on the cotton plants that subjected to four durationsof waterlogging with 1, 3, 6, and 9 days duringflowering and boll-forming stage. The leaf reflectance, gas exchange, and chlorophyll fluorescence of the four leaves from thetop of cotton plants were measured after waterlogging and following,as well compared with non-waterlogged plants. Resultsshowed that：1) Net photosynthetic rate (Pn) decreased significantly after the 1th day of waterlogging, whereas the factorsleading to Pn reduction varied with the duration of waterlogging. The ability of cotton to fixcarbon decreased significantly asthe waterlogging duration less than 3 days. The stomatal factor was the principal factor leading to Pn reduction within 3-6 daysof waterlogging, whereas the stomatal and non-stomatal factors were responsible for C fixation as the durationof waterlogginglonger than 6 days. 2) After the 1th day of waterlogging, the significant decrease indices were the actual PSII photochemistryefficiency (ΦPSⅡ), apparent photosynthetic electron transfer rate (ETR), and photochemistry quenching coefficient (qP),whereas the increase in the non-photochemistry quenching coefficient (NPQ). After the 3rd day of waterlogging, the initialfluorescence (Fo) increased significantly, and the maximum photochemistry efficiency (Fv/Fm) decreased after the 6th day ofwaterlogging. Showing that PSⅡreaction center of the cotton leaves was destroyed by waterlogging, where the transfer rateofelectrons and its efficiency were significantly reduced, leading to the decrease in the conversion rate of light energy, as wellthe distribution part of light energy that absorbed by PSⅡ antenna pigments for photochemistry electron transfer, whereas thepart that consumed by heat increasedsignificantly. Under the waterlogging stress, the share of light energy that used tophotochemical reaction, share(P) was reduced significantly, while the invalid dissipation(the light energy share used inantenna heat dissipation(D) and used in PS Ⅱ reaction center non-photochemical dissipation(E)) significantly increased,resulting the decrease in the utilization efficiency of light energy. There were strong non-linear relationships between thedurations of waterloggingwith the increasing rate of D and E, and the reduction rate of P. 3) The PRI values decreasedsignificantly, while FRI=R600 / R690 and FRI=R740 / R800 increased significantly after the 3rd day of waterlogging. Under thewaterlogging during the flowering and boll-forming stage, the PRI, FRI=R740/R800, FRI=R740/R800, gas exchange parameters,chlorophyll fluorescence parameters demonstrated a linear relationship, indicating the hyperspectral models were feasible topredict the dynamic effects of the waterlogging damage on the gas exchange and chlorophyll fluorescence of the fourth leaffrom the top of plants. By comparison, the hyperspectral models were verified by high precision on simulating Pn and Gsdynamics in gas exchange and Fo, Fv/Fmand NPQ dynamics in chlorophyll fluorescence. The determination coefficient (R2),normalized root mean square error (NRMSE) and sensitivity of spectral parameters to waterlogging have confirmed that theestablished hyperspectral model involving PRI are suitable to simulate Pn, Gs, Fo, Fv / Fm and NPQ during the short-termwaterlogging duration at the late reproductive growth period of cotton plants.