In order to detect low-flying small targets in complex sea condition effectively, we study the chaotic characteristic of sea clutter, use joint algorithm combined complete ensemble empirical mode decomposition (CEEMD) with wavelet transform to de-noise, and put forward a detection method for low-flying target under the sea clutter background based on Volterra filter. By CEEMD method, sea clutter signal which contains small target can be decomposed into a series of intrinsic mode function (IMF) components, pick out high-frequency components which contain more noise by autocorrelation function, and perform wavelet transform on them. The de-noised components and remaining components are used to reconstruct clear signal. In view of the chaotic characteristics of sea clutter, we use Volterra filter to establish adaptive prediction model, detect low-flying small target hiding in sea clutter background from the prediction error, and compare the root mean square error (RMSE) before and after de-noising to evaluate de-noising effect. Experimental results show that the joint algorithm can effectively remove noise and reduce the RMSE by 40% at least. Volterra prediction model can directly detect low-flying small target under sea clutter background from the prediction error in the cases of high signal-to-noise ratio (SNR). In the cases of low SNR, after de-noised by joint algorithm, Volterra prediction model can also detect the low-flying small target clearly.