Subsequently, he was named president of Feng Chia University, where he served until his 1998 appointment as minister of the National Science Council.

As head of the NSC, Huang advocated for research into aftershocks and mapping of the Chelungpu fault, on which the epicenter of the 1999 Chi-Chi earthquake sat.

[1][2] Near the end of his term in 2000, Huang promised to resolve an investigation into United Microelectronics Corporation, which had built a plant in 1998 without submitting an environmental impact assessment for government approval.

[4] Upon leaving the NSC, Huang joined the John Tung Foundation, and was a proponent of suicide prevention and mental health initiatives.

[10] In July 2014, Huang resigned as CPBL commissioner due to a contract dispute with MP & Silva, the company responsible for arranging television broadcasts of league contests.