The radar radiation wave is effected by sea tropospheric ducts and echo multipath effect in the propagation，and waveguide effect makes radar beam to deviate from real position. Multipath effect leads to amplitude-phase vector superposition of radar echo on the array，and the height measurement accuracy of radar is limited. Aiming for height measurement error of shore based radar at the sea direction，a method is proposed in which the atmospheric parameters are inverted to improve radar altimeter accuracy. The method is based on the target track information of radar and height information of the Secondary Surveillance Radar, and the atmospheric correction parameters are fitted by the radar altimetry formula，the modified atmospheric parameters instead of the original k coefficient of radar data processor altimetry formula. The Matlab software is utilized to count the variation of radar height measurement accuracy before and after the correction of the atmospheric parameters over the sea direction. The test results show that the radar height measurement accuracy is increased by 50.8% after the atmospheric parameters are corrected.