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I am learning to use VASP and doing a test for an orthorhombic crystal. I get some un-physical results and find that nearest-neighbor list in the "OUTCAR" is wrong. I recalculate the nearest-neighbor list using my own code and yield correct answers. Is there anything I should or should not do in the "INCAR" and "POSCAR" to eliminate the problem?

the distance between two atoms is calculated from the length of the vector connecting them.
Your POSCAR must be unreasonable. Please have a look in the online handbook how to set up a POSCAR file correctly.
Mind that
--) the units of length in vasp is Angstroem
--) the difference between direct and carthesian coordinates
--) vasp is based on periodic boundary conditions.

I have the same problem with NN, as the guofengw question of 2007.
Thanks

have you compared the values with a third party (eg VESTA, note that you need direct coordinates for that program)