In this letter, a novel design of two-dimensional (2-D) zero reference codes (ZRCs) based on parametric minimum cross entropy (PMCE) is proposed to generate 2-D optical zero reference signals (ZRSs) with low second maximum for grating alignment systems. An optical ZRS is necessary to obtain an absolute measurement in grating alignment systems. A method to acquire an optical ZRS is by means of illuminating two identical superimposed ZRCs. Because the movement between the two ZRCs is in two-axis, 2-D ZRCs are required. However, they are hard to design due to the high computational complexity, especially for large codes. The proposed PMCE method not only reduces the second maximum of 2-D optical ZRSs, but also decreases the computational complexity. Simulation results indicate that there are 8.33%∼ 22.22% reductions in the second maximum of several 2-D optical ZRSs, as compared with those of the recently proposed cross-entropy (CE) method. The PMCE method proves to be a powerful tool for the design of 2-D ZRCs.