In the current context of rising trade protectionism, deeply understanding the impacts of COVID-19 on economy and energy has important practical significance for China to cope with external shocks in an uncertain environment and enhance economic resilience. By constructing an integrated economic and energy input-output model including the COVID-19 shock, this paper assesses the impacts of COVID-19 on China’s macro-economy and energy consumption in the context of trade protectionism. The results are shown as follows. First, in the context of protectionism, the outbreak of COVID-19 in China would cause a 2.2–3.09% drop in China’s GDP and a 1.56–2.48% drop in energy consumption, while adverse spillovers from global spread of COVID-19 would reduce its GDP by 2.27–3.28% and energy consumption by 2.48–3.49%. Second, the negative impacts of domestic outbreak on China’s construction, non-metallic mineral products, and services would be on average 1.29% higher than those on other industries, while the impacts of global spread of COVID-19 on export-oriented industries such as textiles and wearing apparel would be on average 1.23% higher than other industries. Third, the effects of two wave of the pandemic on China’s fossil energy consumption would be on average 1.44% and 0.93% higher than non-fossil energy consumption, respectively.