Over the past decades, blackleg of canola or phoma stem canker caused by Leptosphaeria maculans (anamorph Phoma lingam) has been one of the limiting factors in the production of canola around the world. The general investigation of metabolic profiles using metabolomics approach is one of the strongest methods for identifying mechanisms at the metabolic level, including mechanisms of pathogenisis. In this study, in order to identify the metabolic pathways involved in pathogenesis, changes in metabolic profiles resulting from the interaction P. lingam (Phkv102 isolate) and the susceptible canola cultivar Hyola 401 were investigated by GC-MS chromatography using the polar fraction. Under completely controlled conditions, 14 days after planting, in the dicotyledonous stage, the plants were inoculated by 107 spores per ml suspensions and water (control) by drop-wound method, respectively. The tissue samples were taken 48 hours after inoculation and were shock frozen immediately. Metabolites were extracted using methanol as solvent, identified and quantified with GC-MS and subjected to statistical analyses. Results indicated that 26 metabolites showed significant difference over their controls at P≤0.2, which is caused by changes in 13 metabolic pathways. These metabolic pathways related to the metabolism of sugars, amino acids, organic acids, fatty acids and glucosides. Infection of canola cultivar Hyola 401 to P. lingam leads to a change in pathways related to the host cell wall. In this interaction, two pathways involved in the reinforcement of the cell wall (Cellulose biosynthesis and Hemicellulose biosynthesis) were suppressed. Three important defence pathways including Ascorbic acid biosynthesis, Proline biosynthesis and Chitinase biosynthesis were also suppressed in canola plants under stress. Glucoside biosynthesis pathway was activated in the infected plants possibly in response to the increased cellular demands for D-Glucopyranoside defense compound. The Jasmonic acid biosynthesis has been severely suppressed, presumably due to increased expression of salicylic acid synthesis. The abundance of glucose, galactose, fructose, mannose, myo-inositol and melbiose were also decreased, suggesting the crucial role of these carbohydrates in pathogenesis by P. lingam in susceptible cultivar.