Fish is one of the most common foods that cause allergic reactions. The study of cross-reactivity among fishes using mass spectrometry (MS) is still limited. We developed a strategy using microfluidic chips coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to evaluate cross-reactivity among fishes. The protocol employed commercial magnetic beads functionalized with anti-human IgE antibodies to carry out the IgEs immunomagnetic separation in blood samples, followed by the capture of allergens from seafood protein extracts in a single-straight microfluidic channel. After elution, the captured allergens were digested and identified by MALDI-TOF MS and high-performance liquid chromatography-tandem mass spectrometry and validated by enzyme-linked immunosorbent assay (ELISA). An investigation of the reproducibility revealed that the protocol can sense well the allergens in a food matrix. Seven fish species were analyzed to evaluate the allergic cross-reactivity among fishes. The commercial ELISA test gave consistent results with the presently developed strategy when the same allergenicity test was performed. Parvalbumins were detected from five of the seven analyzed fishes. The sequence alignment of parvalbumins revealed that the similarity of parvalbumins identified from the analyzed fishes is larger than 64%. Boiling may reduce the allergenicity of fish, as demonstrated by a marginal diminish in the parvalbumin content of crucian carp (Carassius carassius) muscle when boiling with water. The method can potentially be used to predict allergic cross-reactivity among fish species, provide advice and guidance to individuals with a history of seafood allergy, and ensure food safety in the food allergy community.