In addition to the changes already made to the Japanese version and original manga, the following was changes were made for the novel:
At his execution, Gold Roger's crimes are read out to him by a Marine as "treason on the high seas, piracy, pillaging and robbery..." before Roger interrupts him. Roger's specific crimes are not stated in the anime. Additionally, in the novel Roger's speech about the One Piece is provoked by the Marine asking if he has any final words rather than by being asked about it directly by a person in the crowd as it was in the anime.
The two sailor's who find Luffy in a barrel are given the names Shiro and Tomeo. Shiro's introduction explains that he is bored on the ship and wants to find adventure, but regrets this a moment later when Alvida attacks.
In the novel, Coby hands out swords to the rest of Alvida's crew before they attack the cruise ship.