If we're talking about live-action films, the actor who has worked with Christopher Nolan the most is probably Ken Watanabe. He's appeared in three of Nolan's films: Batman Begins, Inception, and The Dark Knight Rises.
Watanabe actually auditioned for the role of Bruce Wayne/Batman in Batman Begins, but didn't get the part. He was cast as Ra's al Ghul instead. Watanabe has said that he really wanted to work with Nolan, so he was happy to get a role in the film even though it wasn't the one he originally auditioned for.
Inception was another film where Watanabe had a small but important role. He played Saito, a powerful businessman who Cobb (Leonardo DiCaprio) and his team attempt to extract information from. Once again, Watanabe did a great job in the role and helped make Inception one of Nolan's best films.
The Dark Knight Rises saw Watanabe return as Ra's al Ghul. This time around, his character played a larger role in the story and he got some great scenes with Christian Bale's Batman. It was clear that Nolan appreciated having Watanabe as part of his cast and crew.
So if we're counting live-action films only, Ken Watanabe is the actor who has worked with Christopher Nolan the most. But if we include animated features, then Hideo Nakata takes that title. He directed both English-language versions of Nolan's The Prestige (2006) and Insomnia (2002).