My cat (Persian) is in heat two months after having given birth! Yes, she has stopped breastfeeding the kittens as they have been adopted. However, in case she mates with my male cat and gets pregnant again, will it pose health complications in the future or should I let nature takes it's course? (I've kept them in separate rooms for the moment). I'm in dire need of answers. Please suggest.
Unless you want to have more kittens I would suggest spaying your cat.
It is not about letting nature take its course, being pregnant and giving birth and even being in heat itself is very stressful for your cat.
Also consider that many animals each year are euthanized in shelters because they are unable to find a home or are brought in by former owners. This also happens to pure-bred animals!
That being said you should give your cat time between pregnancies to get back some energy. Giving birth and feeding kittens takes quite some energy away from your cat so give her time to rest in between. Just like with us humans birthing is draining and stressful for cats.