The interlayer distance optimized for low-loss and low-crosstalk double-layer polymer optical waveguides was investigated to enhance their transmission performance. Simulations were conducted to determine the minimal interlayer distances for double-layer optical waveguides with different core sizes. An optimal interlayer distance of 24 µm was identified for a 20 µm × 20 µm double-layer waveguide, which ensured interlayer crosstalk below -30 dB when roughness remained under 80 nm. The double-layer waveguides were fabricated employing ultraviolet lithography combined with the overlay alignment method. Based on experimental optimization, the important fabrication parameters were optimized, such as a plasma treatment time of 10 s, a core exposure dose of 500 mJ/cm2, and a cladding exposure dose of 240 mJ/cm2. Additionally, the fabricated double-layer waveguides, with an interlayer distance of 24.5 µm, exhibited low transmission losses of less than 0.25 dB/cm at 850 nm and 0.40 dB/cm at 1310 nm, respectively. The low interlayer crosstalk values were less than -52 dB at 850 nm and -60 dB at 1310 nm, respectively. The agreement between the experimental results and the simulation findings indicates that this method offers a promising approach for fabricating double-layer waveguides with good performances.