The present study aimed to reveal the molecular mechanism of T-2 toxin-induced cerebral edema by aquaporin-4 (AQP4) blocking and permeation. AQP4 is a class of aquaporin channels that is mainly expressed in the brain, and its structural changes lead to life-threatening complications such as cardio-respiratory arrest, nephritis, and irreversible brain damage. We employed molecular dynamics simulation, text mining, and in vitro and in vivo analysis to study the structural and functional changes induced by the T-2 toxin on AQP4. The action of the toxin leads to disrupted permeation of water and permeation coefficients are found to be affected, from the native (2.49 ± 0.02 × 10-14 cm3/s) to toxin-treated AQP4 (7.68 ± 0.15 × 10-14 cm3/s) channels. Furthermore, the T-2 toxin forms strong electrostatic interactions at the binding site and pushes the key residues (Ala210, Phe77, Arg216, and His201) outward at the selectivity filter. Also, the role of a histidine residue in the AQP4 channel was identified by alchemical transformation and umbrella sampling methods. Alchemical free-energy perturbation energy for H201A ↔ A201H, which was found to be 3.07 ± 0.18 kJ/mol, indicates the structural importance of the histidine residue at 201. In addition, histopathology and expression of AQP4 in the Mus musculus brain tissues show the damaged and altered expression of the protein. Text mining reveals the co-occurrence of genes/proteins associated with the AQP4 expression and T-2 toxin-induced cell apoptosis, which leads to cerebral edema.