The widespread abandoned saline-alkali soils in the Manas River Basin in northwest China have been reclaimed for cotton cropping in recent decade. However, the temporal dynamics of soil microbial functional genes during the reclamation of abandoned salinized farmlands remains unclear. In this study, the abandoned salinized cotton fields that had been reclaimed for 1, 3, 5, and 7 years were selected to study the temporal dynamics of soil microbial functional genes through metagenomic technology. The abundance of genes involved in C, N, P, and S cycles increased significantly since the reclamation, among them, the abundance of KEGG Pathway genes and Enzymes after the reclamation increased by 29.10 and 30.20%, respectively compared with those of the CK (abandoned salinized farmland). The Shannon index of KEGG Pathway and Enzyme-annotated genes after the reclamation increased by 0.82 and 1.10%, respectively compared with those of the CK. The permutational multivariate analysis of variance (PERMANOVA) and correlation analysis showed that the decrease in soil Na+ content and the increase in soil C/N ratio induced by the reclamation increased the abundance and diversity of soil microbial functional genes. After the reclamation, continuous straw incorporation and fertigation increased the soil C/N ratio, and reduced salinity, thus improving soil quality and soil microbial ecological functions. This study will provide reference for the rational development and utilization of abandoned salinized soils in arid areas.