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Simple Summary: 'Chujv', 'Fubai jv', 'Hangbai jv', 'Jinsi huangjv', and 'Nannong jinjv' are the five most popular tea chrysanthemum cultivars in China. Sustained monoculture often leads to plant growth inhibition and quality deterioration, causing significant economic losses to farmers. Endophytic microbes play pivotal roles in plant growth, development, and diversification. However, the effects of endophytes in various tea chrysanthemum cultivars under field conditions remain unknown. In the present study, the community composition and diversity of endophytic bacteria and fungi in five commercially popular tea chrysanthemums were characterized using high-throughput sequencing and culture-dependent methods. The endophytic microbiomes significantly differed across tea chrysanthemum cultivars and organs (stems and leaves). Importantly, it was indicated by the field study that 4 of 42 isolated endophytes could significantly promote tea chrysanthemum yield. These findings offer novel insights into the endophytic microbiomes of tea chrysanthemums and their potential applications in sustainable cultivation. The endophytic microbiomes significantly differed across tea chrysanthemum cultivars and organs (stems and leaves). The most abundant endophytic bacterial genera were Pseudomonas, Masillia, and Enterobacter in the leaves and Sphingomonas and Curtobacterium 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 Alternaria, Cladosporium, and Sporobolomyces. Specifically, Rhodotorula was dominant in the leaves of 'Jinsi huangjv' and Paraphoma 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 (p < 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 (Bacillus oryzaecorticis), CY2 (Pseudomonas psychrotolerans), JSJ7, and JSJ17 (Enterobacter cloacae) 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. [ABSTRACT FROM AUTHOR]