Human well-being in many countries lags behind the gross domestic product (GDP) due to the rapid changes in the socio-economic environment that have occurred for decades. However, the mechanisms behind this complex phenomenon are still unclear. This study revealed the changes in human well-being in China from 1995 to 2017 by revising the genuine progress indicator (GPI) at the national level and further quantified the contribution of interfering factors that have driven the increase in the GPI. The results indicated that: (1) The per capita GPI of China showed an increasing trend with an annual growth rate of 12.43%. The changes in the GPI followed the same pattern as economic development, rather than presenting the phenomenon of economic growth combined with a decline in welfare that has been recorded in some countries and regions. (2) The increase in human well-being was mainly driven by economic growth, but it was most sensitive to social factors. (3) Increasing income inequality and the cost of lost leisure time contributed obvious negative impacts (24.69% and 23.35%, respectively) to the per capita GPI. However, the increase in personal consumption expenditures, the value of domestic labor, ecosystem service value, and net capital growth accelerated the rise in the GPI, with positive contribution rates of 30.69%, 23%, 20.54%, and 20.02%, respectively. (4) The continuous increase in economic investment and the strengthening of social management due to policy adjustments completely counteracted the negative impacts on human well-being, thus leading to a great increase in the per capita GPI. Such insights could provide theoretical support for decision making and policy implementation to improve global human well-being.