My chihuahua has 3day old pups scared to bathe them. Worried she won't care for them after.

You don't need to nor should you bathe them unless something is wrong. Mum will take care of the cleaning of them.

Are you worried about fleas? There is no other reason to bathe the pups yet. If it is fleas you are worried, you should make an appointment with your vet to find a flea/worm treatment suitable for nursing mothers.

The mother seems to be afraid to clean them?

Is this her first litter? If so, she may not know what to do. Keep an eye on her and ensure that she is at least feeding them.

Some mothers are dirty mothers and won't keep their pups spotless.. Quite honestly, I wouldn't worry about it. They may smell a little when you hold them, but them being a little stinky and "dirty" isn't going to prohibit anything.

However, if you feel that you just absolutely need to clean them... You wash them like you would a 3 day old human infant. Warm water, baby shampoo, avoid their faces at all cost and keep them WARM... Puppies at this age cannot regulate their own body temperature. I had one litter of pups where the mother would have abandoned them if she could.. so those pups had to have baths... and that is what I did...

So it is possible.. just not advisable unless you absolutely have to.

Its her first time maybe she's scared or doesn't know how at least she's feeding them properly.