Yu is the recipient of numerous awards and honors for his work in organic chemistry reaction development, including a MacArthur Fellowship (also known as a "Genius Grant") in 2016. He was elected a member of the American Academy of Arts and Sciences in 2019, a fellow of the American Association for the Advancement of Science and the Royal Society of Chemistry in 2012. In 2013, he received the Raymond and Beverly Sackler Prize in the Physical Sciences.
Yu received the Pedler Award from the Royal Society of Chemistry in 2016, and the Elias J. Corey Award for Outstanding Original Contribution in Organic Synthesis by a Young Investigator from the American Chemical Society. In 2012, he was awarded the Mukaiyama Award from the Japanese Society of Organic Synthesis, the ACS Cope Scholar Award, and the Bristol-Myers Squibb Award. His honors also include the Novartis Early Career Award in Organic Chemistry (2011), Eli Lilly Grantee Award (2008), Amgen Young Investigator's Award (2008), and Sloan Research Fellowship (2008).