A three-channel oceanographic shipborne lidar system is built based on a 532 nm pulse laser. The concentration of chlorophyll-a is measured with this system and the results are compared with that obtained by the commercial chlorophyll fluorometer. The comparison results show that, the correlation coefficient between these results as high as 0.84, which shows a good linear correlation. In order to test and assess the detection performance of this system on the chlorophyll-a concentration of the surface seawater, the preliminary field navigation testing is carried out and the distribution of the chlorophyll-a concentration of the surface seawater along the navigation path is obtained. The results show that, the correlation coefficient between the chlorophyll-a concentration of the surface seawater extracted from the lidar detecting data and the chlorophyll-a concentration of the surface seawater obtained synchronously by the commercial chlorophyll fluorometer can reach to 0.69.