Abstract Background and Aims In our previous study, interspecific grafting of Populus cathayana (C) onto Populus deltoides (D) significantly improved the drought tolerance in grafted plants. However, whether this advantage could be maintained under salt stress conditions and the relative underlying mechanism are unclear. Methods Physiological, long non-coding RNA (lncRNA) sequencing and metabolic analyses were performed to illuminate the mechanism governing the different responses to salt stress between C/D (C grafted onto D) and D/C (D grafted onto C) plants. Key Results Salt stress reduced the growth and biomass of all the grafted plants, with C/D plants showing stronger salt tolerance than D/C plants, as evidenced by their greater biomass production and sugar content, less leaf cell damage and better ion homeostasis. More lncRNAs, mRNAs and metabolites related to carbohydrate metabolism were detected in D/C than in C/D plants. Genes related to metabolism of structural and non-structural carbohydrates were respectively up- and down-regulated in C/D and D/C plants, and the changes of citramalic acid, sorbitol and pyruvic acid contents were strongly supported by their different carbohydrate metabolisms. In addition, the lncRNAs MSTRG.102 and MSTRG.4684, as well as their target genes involved in carbohydrate metabolism, were less significantly down-regulated in C/D than in D/C plants. Furthermore, correlation analysis revealed that MSTRG.7877 and MSTRG.20540 might be key lncRNAs in the grafted plants in response to salt stress. Conclusions Our study demonstrates that by affecting the accumulation and metabolism of carbohydrates, different expression and content of multiple lncRNAs, mRNAs and metabolites, associated with structural and non-structural carbohydrates, led to different growth and salt tolerance between C/D and D/C plants. The improved growth and salt tolerance in C/D plants was closely associated with the altered accumulation and metabolism of structural and non-structural carbohydrates.