I think the main difference is in politeness. Someone saying the first sentence, "Couldn't you help me?" is likely to be a little bit frustrated. For example, a parent carrying heavy boxes and their child is standing on the side and not helping. Someone saying the second sentence is also asking someone for help, but they are doing it in a kind way. To be even more polite, they might say, "Could you please help me?" or "Could you help me, please?"

Which one sounds more natural to you? Will’s explanation is correct. “Could you help me?” is much more common.