In this study, we investigated the allelopathic effect of Secale cereale cultivars on different weeds that grow in the cultivated fields of Perilla frutescens. Two S. cereale cultivars, Paldong and Singhi, were used to test the allelopathic effect on in vitro grown Digitaria ciliaris, Chenopodium album, Amaranthus lividus, Portulaca oleracea, Pinellia ternata and Commelina communis. The results indicated that S. cereale extracts affect callus growth of weeds in terms of fresh weight and percentage of growth inhibition. The inhibitory effects of both S. cereale cultivars combined with grass cover extracts were higher than using grass weeds alone. Concentrations of all identified phenolic compounds were significantly higher in the leaves extracts of Paldong compared to Singhi. Particularly, syringic acid in leaves extract of the Paldong cultivar were 12.87-fold higher than in the Singhi cultivar. The other predominant phenolic compounds such as salicylic acid, p-coumaric acid, vanillic acid, and p-hydroxybenzoic acids were 3.30, 4.63, 3.11, and 1.28 times higher, respectively, in the leaves extracts of Paldong compared to Singhi. Principal component analysis (PCA) results indicated that the composition of phenolic compounds was significantly related to cultivar types and plant parts used. In addition, biomass increase caused increased weed inhibitory capacity of S. cereale both in tillage and no-tillage regimes. These results suggest that the biomass of cover crops negatively influenced weed density.