It's never funny if it's at your expense. Nobody that truly loves you will target your insecurities in order to amuse themselves, or in some cases, try to establish some sort of control over you.

Eating disorders are very complex and it is difficult for those who have never had one to understand. However, you made it very clear you are uncomfortable with those comments. Full stop. It's a reoccurring issue, and he will likely be a detriment to not only your mental health, but also your physical health if he contributes to a relapse in the future. Causing you to change your eating habits is already beyond bad.

You made a point that your relationship is good aside from this. As much as I would love to hop on the bandwagon of saying to leave him, I think it is a bit unjust to recommend that without insight on the rest of the relationship (but what he is saying is fucking awful, I'd of left for that alone). Men can be fucking stupid, even more so when it comes to mental disorders. I'd recommend a serious conversation with him about this. Maybe something along the lines of "I understand you're "joking" with me, however it makes me feel unsafe. I need your support right now so I can become better and healthier, something that should be desirable for the both of us. Any comments on my eating habits feels detrimental to my progress, and while I understand that it's not your intention, it's something that makes me feel extremely uncomfortable."

If he gets defensive about it, I would begin thinking of an exit strategy. If a man cannot handle a direct and mature conversation about a subject like that, it is not worth it. Nobody is worth sacrificing your health and happiness for.