The combined effect of weakly acidic electrolyzed water (WAEW) and modified atmosphere packaging (MAP) treatments on the quality of puffer fish (Takifugu obscurus) during cold storage was studied on aspects of microbiological activity, texture, total volatile basic nitrogen (TVB‐N), trimethylamine (TMA), free amino acids (FAAs), thiobarbituric acid reactive substance (TBARS), ATP‐related compounds and K value, volatile organic compounds (VOCs), and organoleptic properties. As a result, significantly (p < .05) higher inhibitory effects on total viable counts (TVC), H2S‐producing bacteria (including Shewanella putrefaciens), Pseudomonas spp., and lactic acid bacteria (LAB) were observed in WAEW‐treated puffer fish packaged in 60%CO2/5%O2/35%N2 atmosphere than that in air package and vacuum package with/without WAEW‐treated samples. In addition, chemical results showed that WAEW together with MAP treatments were highly efficient in maintaining lower TVB‐N, TMA, and TBARS values in refrigerated puffer fish. Moreover, the presence of WAEW combined with MAP treatments showed positive effects on retarding the relative content of fishy flavor compounds, such as 1‐octen‐3‐ol, 1‐penten‐3‐ol, hexanal, heptanal, nonanal, decanal, (E)‐2‐octenal, and 2,3‐butanedione. As a whole, the combined effect of WAEW and MAP on refrigerated puffer fish is advisable to maintain better quality and extend the shelf life.