This paper intends to explore how the EU has responded to the Covid-19 crisis as a transboundary crisis from the perspective of policy instrument. The Covid-19 crisis in the EU has developed into a comprehensive mega-transboundary crisis involving at least a public health crisis and an economic crisis. After the failure of the initial fragmented responses by the member states, the EU has intervened and taken a great amount of operational measures mainly in three dimensions, that is, health and emergency response, economic response and preparations for the European recovery, which can be encapsulated into four types of policy instruments: information, authority, finance and organization. It can be found that the EU governance of Covid-19 crisis has changed from the simple multilevel instrument mix to the complex multilevel policy mix, which means a change from national governance to the EU-level governance. The choice of policy instruments by the EU in response to the Covid-19 crisis is not only the result of the functional logic of a transboundary crisis, but of the institutional supply logic of the EU governance system, which is inseparable from the autonomous actions of the EU institutions and member states.