Nitrogen cycle is an important process in the circle of soil ecosystem elements, and nitrification has significant effect on soil nitrogen cycling. The main completer of nitrification is nitrification microbial communities. Soil microorganisms are vital components of wetland ecosystem. They can indicate the variations of wetland ecological environment, and this helps us to have the correct understanding of nitrogen cycle and pollution purification function in wetland ecosystem. This paper tries to study nitrification microbial communities in wetland soils from the perspective of hyperspectral remote sensing technology, based on the monitoring mechanisms of soil nitrogen spectrum. The study explores hyperspectral estimation techniques for nitrification microbial communities in wetland soils, and it can provide a new technical approach to estimate the temporal and spatial distribution of nitrification microbial communities. The study adopted most probable number method (MPN) to count the numbers of ammonia oxidizing bacteria and nitrite oxidizing bacteria respectively, which were main completers of two independent stages in nitrification. And the total results of both count measurements were used as the values of soil nitrification microorganisms for each sampling area. The estimation models of nitrification microorganism and total nitrogen in wetland soils were developed respectively using spectral transformation techniques, such as log-transformed spectra (LR), first derivative (FD), second derivative (SD), continuum removal (CR) and band depth (BD), and modeling methods, such as stepwise multiple linear regression (SMLR) and partial least-squares regression (PLSR) based on the bootstrap technology. The results indicated that the selected estimation bands of nitrification microorganism and total nitrogen were close (especially for original spectral data (R) and SD spectra) when the modeling method of bootstrap SMLR was used. Compared to the bootstrap SMLR, the bootstrap PLSR achieved higher accuracies for estimating nitrification microorganism and total nitrogen in wetland soils. The spectral transformation technique of SD combined with the modeling method of bootstrap PLSR yielded the highest estimation accuracy to predict nitrification microorganism in wetland soils. The CR spectral data combined with bootstrap PLSR produced the highest estimation accuracy to predict total nitrogen content in wetland soils.