The endophytic microbiomes significantly differed across tea chrysanthemum cultivars and organs (stems and leaves). The most abundant endophytic bacterial genera were , , and in the leaves and and in the stems of the five cultivars. Meanwhile, the most abundant endophytic fungal genera in the leaves and stems of the five tea chrysanthemums were , , and . Specifically, was dominant in the leaves of 'Jinsi huangjv' and was dominant in the stems of 'Jinsi huangjv'. In all cultivars, the diversity and richness of endophytic bacteria were higher in leaves than in stems ( < 0.05). The highest diversity and richness of endophytic bacteria were recorded in 'Chujv', followed by 'Jinsi huangjv', 'Fubai jv', 'Nannong jinjv', and 'Hangbai jv'. Meanwhile, endophytic fungi were less pronounced. Twenty-seven and 15 cultivable endophytic bacteria and fungi were isolated, four isolated endophytic bacteria, namely, CJY1 (), CY2 (), JSJ7, and JSJ17 () showed higher indole acetic acid production ability. Further field studies indicated that inoculation of these four endophytic bacteria not only promoted plant growth and yield but also increased total flavonoids, chlorogenic acid, luteolin, and 3,5-dicoffeylquinic acid levels in the dry flowers of tea chrysanthemums.