In windows, Why the handle value is in multiple of 4?

If I'm not wrong, A handle is an index inside a table maintained on per process basis.

For 64bit Windows, Each entry in this table is made up of 8 byte address to the kernel object + 4 byte of access mask making the entry 12 byte long. However as I understood, for alignment purpose each entry made 16 byte long.

But when you you look at handle opened by a process using process explorer, Value of handle are in multiple of 4. Shouldn't this be in multiple of 16 instead?

A Windows handle is just an index per se, it could be a multiple of 1 in principle. It has been probably more efficient to implent a word (16 bit value) alignment than the byte alignment you're implying.