A compact in-fiber refractive index (RI) sensor based on a step index multimode polymer optical fiber with a micro-hole drilled by a miniature numerical control machine is presented. A good linear relationship between the transmission and RI over a large operating range from 1.335 to 1.475 and a sensitivity of 36 071.43 mV/RIU (RI unit) are found. The relationship between the transmission and the RI of the hole depends on the micro-hole’s diameter and depth. The RI sensor developed in this letter is low-cost, easily fabricated, and capable of continuous measurement.