The floral aroma, sometimes known as an incorporeal gift of flowers, is one of the primary ornamental features of plants. Flowers of genus Tilia are fragrant and have great value for development and utilization. In this study, for the first time, headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) combined with chemometrics were used to analyze the dynamic variations of scent components of the three species from Tilia at different flowering stages. 47 aroma compounds were preliminarily identified, including terpenes, alcohols, ethers, esters, aldehydes, heterocyclics and alkanes. The UpSet diagram displayed great variations in the amount of aroma components at various flowering stages for each species. Partial least squares discriminant analysis (PLS-DA) indicated the proximity of aroma composition characteristics and the significant components that can distinguish the three species from one another. Variable importance projection values (VIP) along with the Kruskal-Wallis non-parametric analysis were performed to identify 9 crucial aroma components, such as α-Farnesene, D-Limonene, Germacrene D, Linalool, etc. In the end, we discovered that, in sharp contrast to T. miqueliana, Tilia cordata Mill. may have a closely related phylogenetic relationship with Tilia tomentosa Moench. by evaluating the aroma similarity rates.