I want to ask that if there any substance that has the different number of electrons and protons at its neutral state
It's certainly possible, you just need other charged particles that aren't electrons or protons.
For example, a positron is positively charged, so something that's made out of an electron plus a positron would work. See e.g. https://en.wikipedia.org/wiki/Onium, or this answer on SE, for a few examples.
Well your question itself is sort of wrong because you assume that individual atoms would have a definite number of electrons... which is usually not the case. In a molecule, electrons can be spread around several nuclei depending on several factors like the atoms' electronegativity or the molecule structure.
In fact, it is not really a matter of how many electrons are around a nucleus but more "how likely" they will be around that nucleus compared to other surrounding nuclei.