The system parameters such as the centroid and pulse width of a laser altimeter system have great effects on its accuracy in ranging and inversion under the condition of a common sea state. Therefore, this paper deduces the functions referred to influencing factors of centroid and pulse width and corrects the received photon function of ocean surface according to the theory of Fresnel diffraction, the character of specular reflection, the statistical regularity of ocean surface profile and the error theory of laser altimeter systems. It gives complete influencing factors on the centroid and pulse width, which include the transmitted and received instruments, nadir angles, pointing jitters and wind speeds. Among them, the first three factors are all system parameters, and the wind speed is a surface characteristic. Combined with the parameters of Geoscience Laser Altimeter System)GLAS, the error of range and the accuracy of pulse width are calculated and analyzed. The results show that the ranging error of GLAS is from 2 to 15 cm, and that of the pulse width is from 0.5 to 3.5 ns under different wind speeds. The obtained conclusion is significant for the design and accuracy analysis of ocean laser altimeter systems.