Both are conditional. You won't understand (if I tell you) - First conditional. Like all first conditionals, this means that there is a real possiblity that the person will tell you. So you might respond by persuading them or reassuring them you will understand. You wouldn't understand (if I told you) - Second conditional. Like all second conditionals in the future, this means that it is very unlikely that the person will tell you. You can, of course, still try to persuade them. But the likelihood they will tell you is much less. This is the grammatical difference. In reality, they might be used interchangeably.

won't is direct speech but wouldn't is conditional - so you won't understand means I know you won't understand, but wouldn't has a meaning that in general I feel you are not able to understand...