In longline fisheries, the habitat and the preferred water layer of the target species should be understood to improve the efficiency of fishing, and the hook depth need to be accurately controlled to set the hooks at the preferred depths of the target species as far as possible. In this paper, the theoretical depths of hooks (D_δ) were calculated by catenary formula. The environmental data, e.g. wind speed (Vw), gear drift velocity (Vg), angle of attack (Qw) (the angle between the prevailing course in deploying the gear and direction that the fishing gear was drifting), and the wind angle (γ) (the angle between the direction of the wind and the prevailing course in deploying the gear), and operation parameters, e.g. line shooting speed (V1), vessel speed (V2), the number of hooks between two floats (Nb), and time interval (t) between two hooks, were collected and the actual hook depth (Df) were measured on the longliners Huayuanyu No.18 and Huayuanyu No.19 in 2005 and the longliner Yueyuanyu No.168 in 2006. The length of float line was 22 m, and the length of branch line was 16 m. The relationship model between the independent variables (D_δ, Vw, Vg, sinQw, sinγ, the hook position code (denoted as δ) ) and the actual hook depths (Df) as dependent variable was built by multiple stepwise regression and the predicted hook depth (D_δ') was calculated by this model. In this paper, applying the built hook depth prediction model, Matlab software was used to programme the operation parameter optimization when V1, V2,γ , Qw, Nb and t were 6-7m/s, 4-5m/s,0-90°,0-90°,23-27,6-8s into the prediction hook depth model, the range of operating parameters (V1, V2,γ , Qw and t) were filtrated to maintain the distribution frequency of the hooks reaching to bigeye tuna preferred water layer (140-240m) to the largest percentage. The results show that: 1) the predicted hook depth model was: D_δ'=D_δ×(0.974+0.097〖sinQ〗_w-0.203 sinγ-0.018δ); 2) the percentage of the hooks at water layer of 140m-240m was ranged from 73.9% to 77.8% (Nb=23-27), with the smallest percentage (73.9%) at Nb=23 and the largest percentage (77.8%) at Nb=27; 3) when the percentage was the largest (77.8%) (Nb=27), the corresponding range of V1, V2,γ , Qw and t were 6-7m/s, 4.4-5m/s,0-90°,0-90°and 6-8s respectively. This paper suggested that 1) the hook depth could be predicted more accurately by multiple stepwise regression; 2) this study method could be used for optimizing pelagic longline operation parameters and improving the fishing efficiency; 3) when targeting the bigeye tuna, it was suggested that Nb should be 27, and other operation parameters should be adjusted according to actual sea conditions; 4) Optimizing the depth of hooks according to this study will help to reduce bycatch of sharks and turtles, etc.