So today I finally opened a new POS biz around my area,although I noticed they is a bigger profit when they is a smaller amount (1k) withdrawn for customers.From 3k up the the profit becomes smaller and the charges goes up as well.

I don't really knows what the issue is,someone should please put me through on what to do.

There are terminals that have a flat rate charge, like from 20,000 and above, they charge 100 naira only but they come with targets, say 200,000 cash in cash out transactions per day. For now, just stick with the existing terminal you're using till you have enough customer base for high volume targets.
Just stick to a little here, a little there for now, steadily the business will grow. Don't charge too much not to drive away customers. Best wishes