Covid-19 has disrupted the normal work order of enterprises. Many employees have experienced unprecedented anxiety, torture and challenges in their physical and mental health, resulting in a decrease in their workplace well-being and job involvement. Employee workplace well-being is an important standard for healthy organizations. In the epidemic situation, it is necessary to resort to new leadership behaviors that can control uncertainty to improve employee workplace well-being. Based on the self-determination theory and the resource conservation theory, this paper discusses the influence of quantum leadership on employee workplace well-being and its transmission mechanism. Through the empirical analysis of 417 valid questionnaires during the period of resumption of work and production in Covid-19, we findthat: Quantum leadership has a significant positive effect on person-organization fit and employee workplace well-being; person-organization fit partially mediates the relationship between quantum leadership and employee workplace well-being; emotional exhaustion positively moderates the relationship between person-organization fit and employee workplace well-being, that is, when employees are in higher emotional exhaustion, the impact of person-organization fit on employee workplace well-being is stronger. This paper provides a new perspective on how to improve employee workplace well-being from the perspective of quantum leadership under the uncertain situation of epidemic. It further expands and enriches the research on the consequences of quantum leadership on the psychological influence mechanism of employees, and provides theoretical support for enterprises to improve employee workplace well-being from the aspects of cultivating quantum leadership, improving person-organization fit and eliminating employees’ emotional exhaustion in management practice.