The number of atoms in the whole Universe seems to be finite, yet the Universe is infinite in dimensions? How it is possible in the Universe?
The number of atoms in the observable universe is finite. But the observable universe is also finite.
The ultimate topology of the whole Universe is unknown. It is not known if the Universe is finite or not. Both options seem hard to stomach, and since it concerns the unobservable, perhaps it lies outside of science...perhaps not.
I think you misunderstanding an important concept. There are a finite number of atoms in the observable universe — that is, the part we can see (notice the lower case "u").
When people say "the universe", they can often refer to the observable universe. Sloppy, I know. The whole Universe (notice the capital "u" here) may be infinite. Also, don't know where you got the idea that the Universe has an infinite number of dimensions.