Two-photon polymerization (2PP) is a powerful technique in fabricating three-dimensional subdiffraction-limited structures. In this paper, 2PP was applied to generate woodpile structures, one kind of photonic crystal, using SZ2080, which is widely used in 2PP due to its negligible shrinkage. First, the relationship between scanning speed, laser power, and resolution was determined through fabricating free-hanging lines by theoretical and experimental study. Based on this relationship, woodpile structures with different period distances were fabricated with high uniformity as shown by scanning electron microscopy (SEM) images. Then optical properties of woodpile structures were investigated using Fourier transform infrared spectroscopy (FTIR) and a quantitative empirical relationship between period distance and band gaps was established. The empirical relationship can be applied to design woodpile photonic crystals for the optical sensors and filters.