Analytic expression of the receiver-aperture-averaged scintillation index (SI) was derived for Gaussian-beam waves propagating through non-Kolmogorov maritime atmospheric environment by establishing a generalized maritime atmospheric spectrum model. The error performance of an intensity-modulated and direct-detection (IM/DD) free-space optical (FSO) system was investigated using the derived SI and log-normal distribution. The combined effects of non-Kolmogorov power-law exponent, turbulence inner scale, structure parameter, propagation distance, receiver aperture, and wavelength were also evaluated. Results show that inner scale and power-law exponent obviously affect SI. Large wavelength and receiver aperture can mitigate the effects of turbulence. The proposed model can be evaluated ship-to-ship/shore FSO system performance.