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1. Band structure from DFT calculations
2. Wannier Band structure of step 1
..
When i plot these two band structures (BS) simultaneously, there is a shift in fermi energy and BS didn't overlap, and fermi level is not zero in both cases. Is it how it should be?

The eigenvalues you get from Wannierization should not be shifted with respect to the eigenvalues you computed in VASP.
What you describe might happen if at some point you shift one of the band-structure and not the other.
Have a look at the eigenvalues in the OUTCAR file and compare with the eigenvalues you get from Wannier90.
Could you share the OUTCAR file, the wannier90.eig and your final data files + plotting scripts you use to plot the band-structure?

Relevant files are being uploaded, DFT as well wannerization based and script too.

As I suspected.
Your BAND.dat file has the eigenvalues shifted by the fermi energy reported in the OUTCAR while the wannier90_band.dat is not.
You can check this yourself. The fermi energy is reported in the OUTCAR:
Fermi energy: -0.9803734921

You can either 'unshift' the eigenvalues in your python script or modify the code you used to generate the BAND.dat file.

You are right,

i am using VASPKIT/SUMO for post processing and both having setting enabled: "fermi-level to be zero"

I switch off this setting and there is no shift in wannerization and simple dft band structure.

thanks