We investigated the roughness-induced scattering loss (LossR) of photolithography-fabricated polymer optical waveguide theoretically and experimentally. Parameters on their effects of the LossR including roughness, waveguide dimension, and operation wavelength were studied. The roughness of the waveguide’s sidewall and top/bottom surface was measured by employing a laser confocal microscope. The results show that the average roughness of sidewall was about 60 nm, which was 3 times of that of top/bottom surface. As a result, the LossR of sidewall was dominant and was 9 times of that of top/bottom surface. Based on the above theory and experimental results, low-loss single mode polymer waveguides operating at the wavelength of 1310 nm with average loss of 0.35 dB/cm were designed and fabricated, which have broad application prospect as the key transmission media of the high-speed high-density optical backplane.