The present paper presents a novel method for simultaneous determination of the three pesticides, carbaryl, carbendazim and 1-naphthol in honey. The excitation-emission matrix fluorescence data from calibration and prediction samples composed a three-way data array and then were analyzed using the second-order calibration method based on the self-weighted alternating trilinear decomposition (SWATLD). The second-order advantage of the SWATLD-based second-order calibration method was exploited, which makes it possible that calibration can be performed even in the presence of unknown interferences. The method was applied to determine the pesticides in the complex matrix of the honey sample. After the calibration step the recoveries of carbendazim and 1-naphthol were satisfactory. The quantification of carbaryl using the second-order standard addition method (SOSAM) based on SWATLD and the high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS) were performed to validate the concentration of carbaryl in honey samples.