This is a great explanation of the difference.

There may be other differences to consider between two similar audio interfaces that feature Thunderbolt or just USB, even from the same manufacturer, apart from conversion quality and latency.

For example, though Antelope Audio sells two very similar seeming products, the older model that doesn't feature Thunderbolt connectivity is still frustratingly unreliable and difficult to troubleshoot when used as a USB computer audio interface, while the newer version works like a dream as a Thunderbolt audio interface (and also works as a USB interface, though not at the same time and with some more latency and/or fewer channels at once). Both units feature ADAT and MADI connectivity, and when connected this way (i.e. to some other unit then connected to a computer) perform identically in terms of conversion quality and latency. This is probably 99%+ to do with the manufacturer, as opposed to a difference in Thunderbolt vs USB, but here it's worth it to most users to spring for the newer model that features Thunderbolt.

tldr - read reviews before purchasing computer audio interfaces