Abstract: The objective of this research was to compare transmission and diffuse reflection modes of visible (VIS)/near infrared (NIR) spectroscopy for detecting black heart in potatoes. Vis/NIR spectra, Vis/NIT spectra and NIR spectra were acquired using hyperspectral image acquisition system, portable transmission spectrum acquisition system and FT-NIR spectrometer, respectively. Partial Least Squares-Linear Discriminant Analysis (PLS-LDA) method was employed to classify the potatoes with or without black heart. Better results were obtained based on Vis/NIT spectra than those on diffuse reflection spectra. The classifying correct rate was 98.46% by using Vis/NIT spectra. The classifying correct rates were 92.31% and 90.77% respectively acquired by hyperspectral image spectrum acquisition system and FT–NIR spectrometer. The results indicated that Vis/NIT spectra method was feasible for detecting black heart in potatoes and transmission mode was better than reflection mode for internal disorder detection. The research can provide references for potato internal defect detection and portable instrument development based on spectroscopy technique.