We used a microtemperature sensor to measure the atmospheric refractive index structure constant Cn2 of near sea-surface and combined ensemble empirical mode decomposition (EEMD) to obtain the intrinsic mode function (IMF) component with different time scales. Furthermore, the analysis of the IMFs’ periods indicates that their mean periods have a high correlation of natural exponential function. Thus, we can derive the space characters based on the ergodicity property of atmospheric turbulence. The result of the Hilbert transform for the IMF component shows the different scale fluctuations near the center frequency of each IMF. Additionally, we can obtain the Hilbert-Huang transform marginal spectrum of conventional meteorological elements and Cn2, and the results indicate that it is superior to the traditional fast-Fourier transform (FFT) in reflecting spectral distribution characteristics of optical turbulence. Further, we analyze the relationship between the Cn2 and conventional meteorological elements under different atmospheric stratification. From above, we can learn more about the space-time characters of near sea-surface optical turbulence, and the study results will provide some references for laser propagation in the marine atmosphere.