The roughness-induced scattering loss (LossR) of photolithography-fabricated polymer optical waveguide was investigated theoretically and experimentally. The effects of the LossR including roughness, waveguide dimension, and operation wavelength on the LossR 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 is about 60nm, which is 3 times of that of top/bottom surface. As a result, the LossR of sidewall is dominant and is 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 1310nm with average loss of 0.35dB/cm were designed and fabricated, which have broad application prospect as the key transmission media of the high-speed high-density optical backplane.