Taiwan is the world’s leading country regarding tuna longline fisheries; the combined catches with those from Japan account for more than half of the global total. However, the bycatch of sea turtles, seabirds, and dolphins in longline fisheries has attracted international concern. Regarding sea turtle conservation, the use of circle hooks in longline fisheries will inevitably become a trend. Meanwhile, Taiwanese fishermen are concerned whether the use of circle hooks will have a negative impact on the catch efficiency of target species. This study was conducted to compare the catch efficiency of circle and tuna hooks by the Taiwanese commercial tuna longline fishing vessels in the eastern Pacific Ocean. The results indicated that if the effects of immersion time were considered, the catch rates of all groups were the same between 4.2-sun circle and tuna hooks. However, the catch rate of 4.0-sun circle hooks was significantly higher than the two types of 4.2-sun circle and tuna hooks. Regarding survival rates, fish caught with circle hooks showed higher survival rates than tuna hooks for total commercial fish, tunas and yellowfin tuna (Thunnus albacares). However, the survival rate was only determined at haulback; the relationship between survival rate and immersion time still needs further investigation. Regarding catch sizes, there were no significant differences in the sizes of bigeye (Thunnus obesus) and yellowfin tuna between circle and tuna hooks. But based solely on mean weight, the value of yellowfin tuna caught using circle hooks may be higher than those using tuna hooks. In summary, the circle hooks used in this study did not show a negative impact on the catch efficiency of Taiwanese longline fisheries, and could show a superior performance than that of tuna hooks. These results could be actively promoted in the industry through the education and training of fishermen; thus enabling Taiwan to comply with international sea turtle conservation trends.