In this study, the difference between wild and farmed salmon production was successfully profiled and differentiated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS) combined with chemometric analysis. The established method based on multivariate analysis mainly involved principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) as the screening and verifying tools to provide insights into the distinctive features found in wild and farmed salmon products, respectively. The discrimination between farmed and wild salmon was accomplished with 100% classification accuracy using chemometric models, 100% identification accuracy was also achieved in distinguishing wild Salmo salar and Oncorhynchus nerka samples. The results of the present work suggest that the proposed method could serve as a reference for detecting salmon fraud relating to wild or farmed production and expand the application of MALDI-ToF technology further into food authenticity applications.