The cloud signals can cause severe wobble of tropospheric ozone concentration in the process of differential absorption lidar measurement of ozone concentration, and bring significant errors. A cloud elimination algorithm is presented. The algorithm effectively eliminate tropospheric ozone wobble by interpolating the ozone concentration in cloud height region. The key point of the cloud algorithm is given through expounding its theoretical basis. The key point of the cloud elimination is the discrimination of cloud signal and accurate positioning of the cloud height. The cloud height information is determined by setting the aerosol extinction coefficient threshold according to the characteristics of the cloud extinction coefficient. The cumulative average of retrieved ozone concentration reduces measurement errors caused by noise. The results show that the correction by interpolation algorithm of ozone measurements in cloud region could overcome the wobble of the ozone measurements caused by clouds.