The study aimed to find a more appropriate method to detect eosinophils in formalin- fixed nasal polyps, since there is no consensus on the standard counting method of eosinophils now. Four 5 μm serial sections were obtained from each 10% neutral formalin-fixed paraffin block and were stained with Chromotrope 2R, Congo red, MBPmAb immunohistochemistry, and conventional hematoxylin and eosin stain respectively. Each section was scanned by the Aperio digital section scanner. The same selected areas were procured for assessment in the serial sections. Chromotrope 2R and MBPmAb immunohistochemistry were specific in detecting eosinophils, which had the lower background staining compared with Congo red and conventional hematoxylin and eosin stain. There were significant differences among the four methods in terms of the eosinophil counting data (p < 0.05), while no significant difference between Chromotrope 2R and Congo red (P = 0.1413). The eosinophil counts in nasal polyps could be more accurately assessed by Chromotrope 2R and Congo red compared with MBPmAb immunohistochemistry and conventional hematoxylin and eosin stain. The popularization of Chromotrope 2R and Congo red may help to unify the eosinophil count in the definition of eosinophilic CRSwNP.