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To clarify: My question is not Why are atoms empty?, my question is Why are they empty so much?

The classical orbit of an atom, roundly speaking, is where the probability to find an electron is highest (or higher than a given number). Here I quote one paragraph from the answer of user ACuriousMind about the emptiness of an atom:

The idea that atoms are mostly "empty space" is, from a quantum viewpoint, nonsense. The volume of an atom is filled by the wave functions of its electrons, or, from a QFT viewpoint, there is a localized excitation of the electron field in that region of space, which are both very different from the "empty" vacuum state.

But this doesn't explain why 99% of an atom is "empty". I mean, why is the distance from the nucleus to the classical orbit (or orbital) so large, 99 times of the radius of its nucleus? Is it because of the mathematical result from the Schrodinger equation?

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As soon as you lose the idea that only "mass" can legitimately fill something, then there is no "empty" anywhere. Even a vacuum is not empty.

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Imagine you have a house, and you have a dog in that house, and you left in the morning. You are now standing in front of that house. Is the house empty? From one point, you could say Yes, the house is 99% empty, only 1% of it is filled with dog, and not air. But then, give me an example of a place with no dog. Alright, you say the bathroom. Bzzt. There is still a chance that the dog is in the bathroom, so you can't say it's EMPTY. Following this logic, the dog could really be anywhere in the house, and the house isn't really empty at all.

Could be completely wrong, but that's what I think after reading ACuriousMind's answer.

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