Neon flying squid (Ommastrephes bartramii) in the Northwestern Pacific Ocean is one of the important economic cephalopods of China mainland, Japan and Chinese Taiwan squid jigging fleets. How to balance the fisheries interests and how to make the scientific fishery management programs by considering the biological, economic and social benefits is one of the important contents in the sustainable utilization of fishery resources. A multi-fleet bio-economic model was established using fishery catch data and correlative fishing economic data from the squid fishery in China mainland, Japan and Chinese Taiwan squid jigging fleets, and simulated the dynamic changes of O. bartramii fishery development during the period 1997 to 2047 in each squid jigging fleet. And it also discussed the dynamic variations of fishing efforts, biomass, yield, fishery profits, and corresponding accumulative yields and profits over 50 years under different management programs in each squid jigging fleet. The results showed that the biomass of the O. bartramii has been decreasing significantly in the first 10 years with the dynamic variation of fishing efforts under all fishery management programs. And it gradually stabilized and maintained at a low level after long-term fluctuations. From the long-term benefits, the accumulative yield and profits were medium under the fishery management program 9, i.e., increasing catchability coefficient of Chinese Taiwan fleet, and this scenario could balance the economic and social benefits in different squid jigging fleets of the three countries and regions, so it was suggested as reference management program of O. bartramii fishery. From the perspective of squid resources conservation, the biomass of O. bartramii was maintained well under the management program 4, i.e., increasing the fishing costs of China mainland squid jigging fleet. So we can optimize this scenario and make it as the reference management program, i.e., increasing the fishing costs of China mainland fleet, while appropriate to reduce the catchability coefficient of the Japanese fleet. This could ensure the biomass of O. bartramii maintain at a higher level.