Discrimination against individual rights and its paradox during the major outbreaks of pandemic have the universality of a normal society and the particularity of a risk society. The key components of the discrimination includes the discrimination of living right, personal dignity, privacy, expression, and the access to medical public welfare resource. ‘The discriminators are the discriminated’ is the substance and core of the paradox of human rights discrimination. The paradox of human rights discrimination is the rational approach to overcome and amend this discrimination, and therefore promote individual rights. Individual rights discrimination in major pandemic is the obstacle of political development, economic prosperity, social progress, and cultural advancement. To overcome individual rights discrimination, the following basic measures should be taken: Continuously strengthening economic development, promoting bioethics education, enhancing and improving the system of fairness and justice, the contractual relationship system, the information flow system and the emergency management system.