There are no fleas or ticks on puppies, use to bath twice in a month with notix shampoo and soap.
Still the scratching problem persists, kindly provide me the reason and solution.

What are you feeding your puppies ? This could also be due to food allergy. Try to keep your puppies on a commercial diet for atleast 6 months or so, making sure you don't feed grain based food items like roti or bread.
Secondly, this could also be due to some chemical that's being used in your house like Phenol. Please cease the usage of this substance. You can use other more pet friendly substitutes available in the market, like Domex.
Thirdly, get your puppies checked with a Vet who will conduct some tests to rule out the possibility of Scabies mites in your puppies. Dogs can carry these mites from one to another. If the mother is scabies infected, it's inevitable for the puppies to be infected as well.
Lastly, bathe your dogs only when you have to. Use a good grooming brush and dry bath shampoo. You can also start adding supplements in the food to help your dogs recuperate from this problem.

I agree with you Navjot Singh,
I am feeding royal canin junior 33, for both the puppies
And there is no such chemical used in my home
Vets are not aware about that problem till now, they suggest me to switch food to home made, like any ragi items, ragi roti.

Once the TOTW is available in stock, i will buy it. By the way can you suggest me some homemade foods that suits puppies?

If you are feeding them RC, you don't have to feed them anything else. It's a complete diet for them. You should feed them RC for atleast 6 months and then gradually shift to home-cooked diet. In the meantime, brush your puppies' coat thoroughly every day.
As a owner, you are doing your home-work and that's very commendable. Don't worry as there's nothing so serious. If you have any doubts, just leave a text on my phone- 9899696419 and I will call you back.