Salvia miltiorrhiza Bge (SMB) has long been used in traditional Chinese medicine to treat cardiovascular and cerebrovascular diseases. Growing clinical usage has led to a huge demand for artificial planting of SMB. Thus, continuous cropping of SMB is an important challenge that needs to be addressed. Continuous cropping can alter the metabolic profile of plants, resulting in poor growth and low yield. In this study, we tried to image the spatial location and variation of endogenous metabolites in continuously cropped SMB using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Spatially resolved expressions of tanshinones, salvianolic acids, polyamines, phenolic acids, amino acids, and oligosaccharides in normal and continuously cropped SMB roots were compared. The expressions of dihydrotanshinone I, tanshinone II A, dehydromiltirone, miltirone, dehydrotanshinone IIA, spermine, salvianolic acid B/E, tetrasaccharide, and pentasaccharide in continuously cropped SMB roots were much lower than those in normal roots. There was little difference in the expressions of caffeic acid and salvianolic acid A in normal and continuously cropped SMB roots. Ferulic acid was more widely distributed in xylem of normal SMB but strongly expressed in xylem, phloem, and cambium of continuously cropped SMB. The spatially resolved metabolite information enhances our understanding of the metabolic signature of continuously cropped SMB and also provides insights into the metabolic effects of continuous cropping in other plants.