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First, I got the accurate total energy with uniformly distributed dense k-points. The obtained CHGCAR file was used to get the BandStructure along special k-points, which resulted in very different location of the Fermi level comparing to the Fermi level obtained from accurate total energy calculation. If I draw the BandStructure, which one of the Fermi levels should I use?

in all ab initio codes, the Fermi level is the enery level of the highest occupied Kohn-Sham state. This of course varies if you change the k-mesh. Usually the band edges are at one of the special k-points (Gamma, R,...), which most probably these were included in the k-mesh of the band structure run.

You should use the Fermi level obtained from the first calculation, because the k-point sampling maps the whole irreducible Brillouin zone. For a band-structure calculation, the k-points are usually along some high-symmetry direction of the Brillouin zone only. Hence, the Fermi level is not accurate in general for your second calculation, just that VASP calculates and prints out the Fermi level whatever.

please read some standard physics textbooks: usually the VBM is at one of the special k-points of the BZ