Will this voltage doubler works with DC input?

How much current? That IC will work to generate -3V from +3V, which you could then connect the -3V to the common (ground) of your circuit ONLY IF the battery is not connected anywhere else but to the ICL7660 and the ground of the ICL7660 MUST NOT be connected to your circuit ground.

But this won't supply much current. The equivalent series resistance goes up as the input voltage goes down.