With the improvement of people's living standard, the demand for by-products such as honey has increased, and there is increasing concern about honey quality and nutritional composition. The chemical composition of honey may be different when bees collect nectar from different plants. Organic acids are important nutritional and active ingredient in honey. However, there is no study with comprehensive methods for detecting the organic acid composition and content in honey. Linden honey is the honey brewed by bees from the flower nectar of linden plants (such as Tilia amurensis Rupr., Tilia mandshurica Rupr.et Maxim.). It is mainly produced in Wanda Mountains, Greater Khingan Mountains (Daxinganling), Lesser Khingan Mountains(Xiaoxinganling), Changbai Mountains and the Russian Far East, with high output and great nutritional value. It is therefore necessary to establish a dataset for the distribution of organic acid content in linden honey. In this study, we used SPE-GC-MS to detect 22 organic acids in linden honey collected from Heilongjiang Province and Jilin Province, with an average total content of 644.3 mg/kg, in which the content of gluconic acid accounted for the largest percentage, followed by L-lactic acid and malic acid.