Parahemionitis arifolia exhibited strong desiccation tolerance enabling it to withstand irregular dry periods in southern Taiwan. Yet, it is poorly understood how desiccation shapes its metabolism. Here, we report metabolic responses to 1- and 3-weeks of dehydration by air drying in this desiccation-tolerant fern. Metabolite profiling and quantitative analysis of water-soluble metabolites in leaf and rhizome extracts were conducted by nuclear magnetic resonance (NMR) spectroscopy. The ¹H NMR metabolite profiles and two dimensional NMR (2D NMR) analysis identified sugars (sucrose, glucose, fructose, and trehalose), amino acids (γ-aminobutyric acid (GABA), alanine, tyrosine, and glutamine), cyclic polyol (quinic acid) and malic acid. Quinic acid was only observed in the leaf samples but was not detected in the rhizome samples. Glucose and fructose contents in rhizomes increased notably with the duration of air-drying. Trehalose content increased in the air-dried rhizomes, though it was detected in much smaller amounts compared to other sugars. The content of GABA increased dramatically in air-dried leaves and rhizomes but was not detected in any fresh samples. The content of sucrose, alanine, and malic acid in leaves and rhizomes increased in response to desiccation. On the contrary, glutamine content in both leaves and rhizomes decreased after air-drying. Based on these results, we conclude that the metabolic response of the fern P. arifolia to desiccation appears to be consistent with most desiccation tolerant plants. The metabolite concentration in rhizomes changed more significantly than in leaves after drying, indicating that rhizomes and leaves have different drought tolerance capabilities.