Evaporation duct is a kind of chaotic phenomenon over the ocean. In this paper, a new nonlinear prediction algorithm, the Darwinian evolutionary algorithm (DEA), is introduced to obtain the specific nonlinear formula P(·) of the chaotic phenomenon. Based on Darwinian natural selection and survival theory, the method first selects a suitable training set of samples, and then produces an initial population before going through an evolutionary process of selection, reproduction and mutation until the optimal individual is found. Finally, a specific expression for a nonlinear chaotic time series is obtained, which can realize the short-term prediction of evaporation duct height (EDH) quickly and accurately. After that, the DEA, the support vector regression (SVR), and the back propagation (BP) neural network were applied to predict the EDH which were formed over the ocean by using sounding data. After interpolation and smoothing of the original data, we selected the first 250 data as training samples and the last 115 data as test samples to test the effect of the EDA algorithm. The results showed that the root mean squared error (RMSE) for the DEA was about 7% less than that of the SVR and 10% less than that of BP neural network; the mean absolute percent error (MAPE) for the DEA was about 9% less than that of the SVR and 15% less than that of BP neural network. In addition, the DEA obtained, for the first time, a nonlinear expression for EDH, which provides an important reference for future research on the evaporation ducts.