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Because in the Kuro arc, Kaya the sick girl he was looking after gave the crew a proper ship (a.k.a the Going Merry) to help with their travels, because they saved her and the whole town from an infamous pirate called Captain Kuro. So Ussop cares for it as he cares for Kaya too (and I think it's also because he's proud that he provided the most important part of the crew except the actual crew).

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