The late, great Jacques Saunière was a huge fan of another late great: Leonardo Da Vinci.
In fact, he was such a big fan that he devoted much of his life to preserving his work—the well-known as well as the obscure. One of his recreations (from diagrams in Da Vinci's personal journals) was the cryptex: a strange, cylinder-shaped object that possessed a number of dials and contained a vial of vinegar with papyrus wrapped around it.
Saunière, the genius that he was, chose this security measure to protect a series of clues that would allow only people well versed in Grail lore to open it. So, the "code" referred to in the title of the book are all the clues that are written in code that Langdon and Sophie have to decipher in order to honor his dying wishes.