Soil conditioners have great potential in saline soil remediation. However, it is still unclear that how soil conditioners affect cotton photosynthesis to improve cotton resistance to saline and alkaline stresses. Therefore, we used the self-developed soil conditioner was used to clarify whether soil conditioner has a repair effect on cotton photosynthesis under saline and alkaline stresses. The photosynthetic performance and chlorophyll fluorescence characteristics of cotton leaves have increased in PY and PJ. Transcriptome and Proteome analysis results showed that Photosystem II protein, Chlorophyll A-B binding protein, Rubrerythrin and Cytochrome B6-F complex Fe-S subunit were up-regulated in the PY and PJ group. All above changes induced by conditioner application promoted chlorophyll biosynthesis, and regulation of the photosynthetic system. This study will deepen our understanding of the molecular mechanism of soil conditioner regulating cotton photosynthetic, and provide reference for saline and alkaline soil remediation in arid areas.