In reference to the conflict man vs. nature, this occurs when Jim Hawkins has to struggle to navigate the boat Hispaniolas to safety as well as the small boat owned by Ben Gunn. Also in Chapter 24, Jim finds himself at the end of the island which includes the island's tallest hill and falls to the sea. The territory that Jim has landed on is very rough and he must figure out a way to cross. He decides to let nature takes its course and let the current take him to the Cape of the Woods. In this sense, he has to trust nature to keep him safe and lead him where he needs to go.
Man vs. self is shown in the difficult decisions Jim must make. He must decide whether or not to desert his crew. Also, when Bob steals the treasure he is overcome with guilt for the decision he made.