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The chlorophyll content of leaves is an important indicator of plant environmental stress, photosynthetic capacity, and is widely used to diagnose the growth and health status of vegetation. Traditional chlorophyll content inversion is based on the vegetation index under pure species, which rarely considers the impact of interspecific competition and species mixture on the inversion accuracy. To solve these limitations, the harmonic analysis (HA) and the Hilbert–Huang transform (HHT) were introduced to obtain the frequency index, which were combined with spectral index as the input parameters to estimate chlorophyll content based on the unmanned aerial vehicle (UAV) image. The research results indicated that: (1) Based on a comparison of the model accuracy for three different types of indices in the same period, the estimation accuracy of the pure spectral index was the lowest, followed by that of the frequency index, whereas the mixed index estimation effect was the best. (2) The estimation accuracy in November was lower than that in other months; the pure spectral index coefficient of determination (R2) was only 0.5208, and the root–mean–square error (RMSE) was 4.2144. The estimation effect in September was the best. The model R2 under the mixed index reached 0.8283, and the RMSE was 2.0907. (3) The canopy chlorophyll content (CCC) estimation under the frequency domain index was generally better than that of the pure spectral index, indicating that the frequency information was more sensitive to subtle differences in the spectrum of mixed vegetation. These research results show that the combination of spectral and frequency information can effectively improve the mapping accuracy of the chlorophyll content, and provid a theoretical basis and technology for monitoring the chlorophyll content of mixed vegetation in wetlands.

UAV Mapping of the Chlorophyll Content in a Tidal Flat Wetland Using a Combination of Spectral and Frequency Indices