Tu Youyou married Li Tingzhao, an engineer she met while at Peking University. Li Tingzhao became a professor at the China Academy of Space Technology. He provided significant support for her throughout her demanding career.

Tu Youyou's dedication to her research often required sacrifices in her personal life. During the critical years of Project 523, she had to leave her young daughter in the care of relatives for extended periods. This reflects the challenges faced by many scientists who dedicate their lives to their work.

Tu Youyou had two daughters. While details about their lives are less publicly known, it's understood that she strived to balance her demanding career with her responsibilities as a mother.