It could be beneficial to reducing the incidental catch of nontarget species, and improving the accuracy of CPUE standardization to study on the effective fishing effort and fishing efficiency of the longline fishing gears. A survey on tuna longline fishery has been conducted in waters near Gilbert Islands from October to December 2009. The traditional and experimental fishing gears were used in the survey. The bigeye tuna (Thunnus obesus) nominal CPUE in the different depth classes were used to estimate its habitat preference. The “deterministic habitat based standardization” was applied to estimate the effective fishing effort of the traditional and experimental fishing gears. The difference of the fishing efficiency between the traditional and experimental fishing gears was tested by the Ttest. This study suggested that: （1）There was significant difference between the nominal CPUE of the traditional gear and that of the experimental gear, and the nominal CPUE of the traditional gear was less than that of the experimental gear;There was significant difference between the nominal fishing effort and the effective fishing effort, and the effective fishing effort was less than the nominal fishing effort; （2）The efficiency of the experimental gear for the bigeye tuna was greater than that of the traditional gear; （3）When the target species was bigeye tuna, the experimental gear was suggested to be used in the operation to increase the fishing efficiency; （4）The different fishing gear has the different fishing efficiency to the same catch species; the distribution of bigeye tuna CPUE in the different depth classes could be used to estimate the habitat preferences of the bigeye tuna and estimate the fishing efficiency of the fishing gear for the bigeye tuna; and the “deterministic habitat based standardization” model could be used in the CPUE standardization to improve the accuracy of the stock assessment for the respective catch species.