The objective of the present study was to investigate the effects of astragalus polysacharin (APS) on the expression profile of long non-coding RNA (lncRNA) during brown adipogenesis of mouse C3H10T1/2 cells. 0.4 g/L APS was added to induction medium, and the 1.5 day brown adipogenic induced cells were used for the library construction and sequence, we screened differential mRNAs and differential lncRNAs, and analyzed the differential mRNAs and the target genes predicted by differential lncRNAs cis and co-expression were analyzed functionally. In addition, the expression levels of three random lncRNAs and three mRNAs were detected by fluorescence quantitative PCR to verify the accuracy of the sequencing results. The results indicated that a total of 13 450 lncRNAs and 57 776 mRNAs were obtained by sequencing. The reliability of the sequencing data was good by analyzing the expression amount, length, number of exons and pair repeatability. A total of 153 differentially expressed lncRNAs and 1 227 differentially expressed mRNAs were screened. The results showed that the differential mRNAs GO annotation was enriched in 53 functional categories, and the KEGG analysis was enriched in 343 pathways. The GO annotations of target genes predicted by cis and co-expression of differential lncRNAs were enriched in 34 and 33 functional categories, respectively, and the molecular function items were the same; KEGG analysis showed that many genes were enriched in the signal pathway of fat metabolism and fat differentiation, especially in glucagon and cAMP signal pathway. In conclusion, APS could effectively affect lncRNA expression profile of brown adipogenic induced C3H10T1/2 cell, which will further provide fundamental data for understanding the effect of APS on stem cell differentiation.