Considerable attention has been paid to the establishment of an appropriate cropping patterns for the restoration of saline-alkali lands. This study’s goal was to explore changes in nitrogen-cycling (N-cycling) gene (nitrogen fixation: nifH; nitrification: AOA, AOB, and nxrB; denitrification: narG, norB, and nosZ) abundance of three cropping patterns at two soil depths in saline-alkali soils. Results showed that rotation and mixture promoted soil nutrients. N-cycling functional genes were significantly influenced by soil depths and cropping patterns. Compared with monoculture, rotation decreased the abundance of nifH, AOA, narG, and nosZ and increased the abundance of AOB; mixture decreased the abundance of AOA, narG, and nosZ and increased the abundance of AOB and nxrB in the 0–15 cm soil depth. Rotation increased all genes abundance; mixture increased nosZ abundance and decreased nxrB abundance in 15–30 cm soil depth. Soil protease, cellulase, nitrate reductase, pH, AK (available potassium), and AP (available phosphorus) were important factors influencing N-cycling gene abundance. In conclusion, rotation and mixture not only reduced soil salinity but also improved soil fertility and nitrogen cycling. These findings can provide some theories for the sustainable development of N-cycling during the restoration of saline-alkali soils.