[1][2] Yu has designed and co-designed several award-winning games, most famously Spelunky, Aquaria, and Eternal Daughter.

After graduating college with a degree in computer science, Yu moved to San Francisco and worked as a freelance illustrator.

The collaboration with Holowka later led to the formation of the company Bit Blot and the release of Aquaria in 2007, which was a big success and won the Seumas McNally award at the 2007 IGF.

According to Yu, "Not only did Aquaria sell well enough that [Alec Holowka and I] could continue making games full time, but the positive feedback we received from players and critics also validated us as artists and helped to put to rest our doubts about whether we were making something worthwhile."

In 2014, Yu designed the card game Time Barons with Jon Perry.