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He was named the head of the Council of Labor Affairs in 2005, and stayed on in the Su Tseng-chang cabinet. Under his leadership, the CLA sought to decrease the number of job-related deaths and injuries causing disabilities. In 2008, Lee was named the Secretary-General of the Democratic Progressive Party and deputy Yunlin County magistrate under Su Chih-fen. He resigned the deputy magistracy to run in a legislative-by election caused by the annulment of Chang Sho-wen's election. However, Lee lost a primary to Liu Chien-kuo. He was reelected to the Legislative Yuan in 2012. During the summer of 2015, Lee accompanied DPP chairperson and 2016 presidential nominee Tsai Ing-wen on her visit to the United States, along with DPP General Secretary Joseph Wu. Lee was named Tsai's Environmental Protection Administration minister after she won the election. He stated that his goal was to transform the EPA into a full-fledged ministry within 18 months of taking office. On 1 December 2018, Lee stepped down from the EPA.

Lee was elected to the Legislative Yuan in 1996. He then became the youngest convener of the Democratic Progressive Party (DPP) caucus in the legislature. Following DPP’s successful presidential election in 2000, Lee was appointed by President Chen Shui-bian to be the Deputy Representative of the Taipei Economic and Cultural Representative Office (TECRO) in the U.S. and then Secretary-General of the Executive Yuan. He was then named the DPP candidate for Taipei City's 2002 mayoral election, losing to incumbent mayor Ma Ying-jeou in a landslide.

After returning to Taiwan through illegal channels and avoiding intelligence agents for fourteen months, Lee was arrested in September 1991, and charged with violation of Article 100 of the Criminal Code. He was released in May 1992, after would-be colleagues at National Taiwan University intervened on his behalf. Revisions to Article 100 were also passed that month, and meant that evidence of possible threats had to be submitted to the Commission of Violence prior to indictment or arrest.

Lee Ying-yuan (Chinese: 李應元 ; pinyin: Lǐ Yìngyuán ; Pe̍h-ōe-jī: Lí Èng-goân ; born 16 March 1953) is a Taiwanese politician. He was elected to the Legislative Yuan in 1995 and stepped down in 2000. In 2005, Lee was appointed the Minister of Council of Labor Affairs, which he led until 2007. Lee has also served as Secretary-General of the Executive Yuan and the Democratic Progressive Party, and was reelected to the Legislative Yuan in 2012. He was appointed the Minister of Environmental Protection Administration in 2016.

Lee Ying-yuan was born into a family of farmers in 1953. He studied public health at National Taiwan University and earned a master's degree in health policy from Harvard University before receiving his PhD in health economics in 1988 from the University of North Carolina at Chapel Hill. Upon Lee's graduation, he was slated to teach at NTU, but was placed on a blacklist and barred from returning to Taiwan by the Kuomintang-led government, stemming from his pro-democracy activities in the Formosa Incident during Taiwan's martial law period. During Lee's time as a student in the United States, he was also an active member of the World United Formosans for Independence, which attracted more of the KMT's attention.