Understanding the trade-off relationships between ecological, economic and social objectives is important in designing policies to manage or restore ecosystems. Using the northern South China Sea (NSCS) as a case study, we explore the trade-offs between conservation and socio-economic objectives in managing fisheries in tropical marine ecosystems. Using a numerical optimization routine and ecosystem modelling (Ecopath with Ecosim), the study shows that current management of the NSCS is sub-optimal both in terms of conservation and economic objectives. Therefore, improvement in both conservation status and economic benefits can be achieved by reducing fishing capacity. However, the implementation of conservation plans may be hindered by the reduced number of fisheries-related jobs and the lack of alternative livelihoods. Similar trade-offs are apparent in many tropical marine ecosystems. Thus, this paper supports claims from previous studies that solving the alternative livelihood problems appears to be a priority for improving management and conservation in these ecosystems. A buy-back scheme that is funded by fishers might be effective in reducing fishing capacity. However, public funds are required if management objectives focus strongly on conservation. This might be justified by the direct or indirect benefits to society that could be provided by well-conserved ecosystems. This study highlights the conflict between maximizing conservation and social objectives, although win–win solutions between conservation and economic objectives may be possible.