A vehicle body joint structure includes a roof side member extending in a front-rear direction from a side of an upper portion of a vehicle body, a pillar member extending in an up-down direction and matched to a front end or a rear end of the roof side member, a roof rail member laterally extending from the upper portion of the vehicle body and matched with the front end or the rear end of the roof side member, and a connector disposed at the front end or the rear end of the roof side member and fixing the roof side member, the pillar member, and the roof rail member.