In this study, we aimed to investigate the anti-inflammatory activity of polypeptides Asp-Asp-Asp-Tyr (DDDY) and Asp-Tyr-Asp-Asp (DYDD) discovered in fermentation media from Dendrobium aphyllum towards LPS-induced RAW264.7 macrophages. Synthetic D. aphyllum fermentation polypeptides were prepared and subjected to experimentation. Concentrations of fermentation polypeptides that resulted in the highest cell proliferative activity were screened for using the methyl thiazolyl tetrazolium (MTT) assay. The effects of fermentation polypeptides on the phagocytic activity of RAW264.7 cells were determined using neutral red phagocytosis assay. Cell differentiation and changes in morphology were observed under an inverted microscope. Secretion levels of NO, cytokines IL-1β, IL-6, and IL-10, and tumor necrosis factor-alpha (TNF-α) were determined by enzyme-linked immunosorbent assay (ELISA). Fermentation polypeptide concentrations of 12.5, 25, 50, and 100 μg/mL exerted no cytotoxic effects and promoted cell proliferation. Approximately 100 μg/mL DDDY and DYDD and 1 μg/mL LPS enabled cell activation and enhanced RAW264.7 cell phagocytic ability, with relative phagocytic rates of 2.05%, 1.97%, and 2.19%, respectively. An LPS-induced RAW264.7 cell inflammation model was constructed, in which both types of fermentation polypeptides effectively inhibited cell differentiation and restored normal cell morphology. The respective NO secretion capacities of cells in the 100 μg/mL DDDY and DYDD treatment groups decreased to 0.41- and 0.49-times, respectively, compared with that of the LPS group. DDDY and DYDD also significantly and dose-dependently increased anti-inflammatory cytokine secretion and decreased the secretion of pro-inflammatory cytokines. Therefore, DDDY and DYDD exert anti-inflammatory effects on the LPS-induced RAW264.7 macrophages. The results of this study may provide a scientific basis for future investigations of the anti-inflammatory mechanisms of fermentation polypeptides.