Dendrobium catenatum, which belongs to the Orchidaceae family, has been used as a traditional medicine and healthy food in China for over 2000 years, and is of enormous economic value. Polysaccharides and flavonoids are two major functional ingredients in D. catenatum stems that contribute to its health benefits. D. catenatum lives in close association with endophytic fungi, but the literature regarding the further relations between them, especially the fungal-induced accumulation of metabolites in the host plant, is sparse. Our previous study showed that Pestalotiopsis sp. DO14 isolated from D. catenatum improved the host plant growth and metabolite accumulation. This study was performed to investigate dynamic variations of the growth traits, key metabolites (polysaccharides and flavonoids), and expression of key genes of D. catenatum under conditions of the DO14 colonization. Colonization with DO14 promoted D. catenatum growth as indicated by increased leaf area, mid-stem thickness, and plant height. The content of polysaccharides, mannose, and sucrose increased even without DO14 entering the host cells or forming a mature symbiotic relationship concurrent with improved photosynthesis rate. Furthermore, DO14 induced upregulation of genes involved in sugar and flavonoid metabolism, especially phosphoenolpyruvate carboxykinase (PCKA), chalcone synthase (CHS) and UDP-glycose flavonoid glycosyltransferase (UFGT). These observations suggested that endophytic fungi induce the accumulation of polysaccharides and flavonoids by plants, increasing the efficiency of carbon assimilation and carbon turnover. The findings of this study provide insight into the mechanisms underlying Orchidaceae–endophyte interactions, and suggest potential novel applications of endophytic fungi in D. catenatum breeding to improved plant quality.