A compact photonic sensor using a perforated waveguide (PW) that functions as a bimodal interferometer (BiMI) is developed for affinity sensing. A 2D array of holes is formed on the bimodal region of the waveguide. The PW is designed to allow 1.31 µm wavelength light to transmit, harnessing the strong optical intensity distribution inside the holes to enhance the sensitivity of the sensor. Numerical simulations show that the PW-BiMI outperforms a nonperforated BiMI in surface sensitivity by 7.6 times. A molecularly imprinted polymer for human serum albumin (HSA) is synthesized and coated on the PW-BiMI. The sensitivity and detection limit for HSA achieved using a 100 µm long sensor are 154 nm µm−1 and 20.4 µg mL−1, respectively. Compared with a BiMI of equivalent length, the PW-BiMI sensor would have a 22 times larger surface sensitivity, and the detection limit would be decreased to 31%. The PW-BiMI sensor has potential for application in label-free biosensing with a small volume of solution.