A kind of method with immune ant colony algorithm (IACA) was applied for ship parts nesting problems. Graphics coding and pretreatment method of ship parts were proposed. A method of combination and filling transformed ship parts nesting problem into orthogonal rectangular nesting problem. An automatic nesting system was realized by use of remaining rectangular matching method and orthogonal approach grafting algorithm. A specific example was given according to the proposed algorithm, the nesting results prove that it is feasible for ship parts optimization nesting problem with IACA.