Discrimination of individual rights and its paradox during public health emergencies have the universality of a normal society and the particularity of a risk society. The critical components of discrimination include the discrimination of the right to life，human dignity，privacy，expression，and access to public health care resources.“The discriminators are the discriminated” is the core of the paradox of human rights discrimination. The paradox of human rights discrimination is the rational approach to overcoming this discrimination and promoting individual rights. Individual rights discrimination in a public health emergency is an obstacle to political development，economic prosperity，social progress，and cultural advancement. The following basic measures should be taken to avoid individual rights discrimination: continuously strengthening economic development and promoting bioethics education. We should also focus on enhancing the system of fairness and justice，the contractual relationship system，the information flow system，and the emergency management system.