The interactions between microbes and plants are governed by complex chemical signals, which can forcefully affect plant growth and development. Here, to understand how microbes influence Houttuynia cordata Thunb. plant growth and its secondary metabolite through chemical signals, we established the interaction between single bacteria and a plant. We inoculated H. cordata seedlings with bacteria isolated from their roots. The results showed that the total fresh weight, the total dry weight, and the number of lateral roots per seedling in the P. fluorescens-inoculated seedlings were 174%, 172% and 227% higher than in the control seedlings. Pseudomonas fluorescens had a significant promotional effect of the volatile contents compared to control, with β-myrcene increasing by 192%, 2-undecanone by 203%, decanol by 304%, β-caryophyllene by 197%, α-pinene by 281%, bornyl acetate by 157%, γ-terpinene by 239% and 3-tetradecane by 328% in P. fluorescens-inoculated H. cordata seedlings. the contents of chlorogenic acid, rutin, quercitin, and afzelin were 284%, 154%, 137%, and 213% higher than in control seedlings, respectively. Our study provided basic data to assess the linkages between endophytic bacteria, plant phenotype and metabolites of H. cordata to provide an insight into P. fluorescens use as biological fertilizer, promoting the synthesis of medicinal plant compounds.