In order to understand the suitable operation parameters of tuna longline in South China Sea, catch rate in different water layers were estimated for Thunnus obesus and Thunnus albacre based on 8 voyages of tuna longline survey data from June 2010 to February 2013 in South China Sea. With adjustment of three operation parameters - float line length hf, numbers of hook between two floats n and sag ratio k as the object of study, matching degree of hook distribution frequency with tuna harvesting distribution frequency in different water layers was measured by least square method. The most suitable operation structure of logline was found as the sum of squared frequency difference was minimized. The result showed that hf=34, n=25, k=0.68 were the most suitable for targeting Thunnus obesus; hf=10, n=14, k=0.71 were the most suitable for targeting Thunnus albacre; hf=8, n=27, k=0.69 were more suitable for targeting both species.