Helianthus annuus L. is one of the four largest oil crops in the world. In order to understand the molecular mechanism of biosynthesis of major fatty acid components in sunflower, high oleic acid inbred line J9 and low oleic acid inbred line P50 were selected as research materials; The fatty acid composition and content of different samples after pollination were determined by liquid chromatography in the same sampling experiment of staggered sowing; RNA Seq technology was used to sequence different samples to obtain gene expression data related to fatty acid synthesis. Based on meteorological data, liquid chromatography data, sunflower genome data and transcriptome data, bioinformatics methods were used to analyze relevant data. The results showed that: (1) The composition and content of fatty acids in high oleic sunflower materials were less affected by temperature, while the low oleic sunflower materials were easily affected by temperature; (2) The number of high expression genes in 12 samples of J9 and P50 is about 7500, while the number of medium and low expression genes is equivalent, twice that of high expression genes, about 15000; (3) After removing the duplication of variety specific expression genes and inter variety specific expression genes, 15885 were obtained in J9 and P50 in the - CK and S data sets. 403 DEGs directly related to lipid metabolism obtained by GO function enrichment were mapped to the KEGG metabolic pathway related to lipid metabolism. A total of 29 DEGs were directly involved in 19 related KEGG pathways. This study will provide new information for further understanding the molecular mechanism of sunflower fatty acid metabolism.