Since May 2008, relations between the People’s Republic of China and the Republic of China on Taiwan have improved significantly, but the two sides are now confronted with issues more difficult than before. One that has received more attention after the mass protests in Taiwan’s 2014 Sunflower Movement is human rights. Civic groups in Taiwan often criticise the two governments for sidelining human rights issues in their exchanges despite some continuing discussion on the rights of their own nationals detained by the other side. This article, focused on an under-analysed area in China–Taiwan relations, examines the extent to which human rights-related issues have been addressed as well as avoided in negotiations across the Taiwan Strait. It then discusses various proposals that have emerged in Taiwan in recent years calling for a greater emphasis on human rights in cross-strait relations. Notably, some of these proposals are intertwined with Taiwan’s politics and claims relating to its sovereignty. In conclusion, the article offers a policy recommendation for Taiwan to seek to meaningfully integrate human rights practice in cross-strait cooperation.