The drought resistance mechanism of Matteuccia struthiopteris (L.) Todar. and Athyrium multidentatum (Doll.) Ching were measured under natural drought exposure. The results showed that the two edible fern species showed stronger resistance in the early stages of drought, mainly expressed as the decrease of relative leaf water content (RLWC), increase of osmotic substances, secondary metabolites such as flavonoids (FC), total phenols (TPC), proantho cyanidins (PCC) content and enzyme activity (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)). The higher RLWC, FC, TPC, PCC and abscisic acid (ABA) content and lower H2O2 content indicates the stronger non-enzymatic antioxidant system and drought resistance of A. multidentatum. However, the proline (Pro) content changed slowly, and the synthesis of soluble protein (SP), total phenols, proantho cyanidins and ABA, SOD activity of two fern species were inhibited in the late stages of drought stress. This study can provide a scientific basis for the cultivation and utilization of edible fern species under forest in Northeast China.