The $1.5 billion plan includes an aerial park that will sit atop three levels of bus platforms and retail stores.
It also calls for building a train station on the basement level of the complex. That station will serve Caltrain and California's proposed high-speed rail system.
Crews will begin demolition of the existing, 1930s Transbay Terminal in a few months.
Commuter buses will use a temporary terminal until the new facility opens in 2017.