To investigate different method of soil fertilization and their effects on physiological growth indices a filed experiment was carried out on Fennel (Foeniculum vulgare Mill.) Clmedicinal plant, in Alborz Research complex, (NPK), used in commercial agriculture systems, a mixture of different ratios of fertilizers and manure, used in intermediate systems as well as different levels of manure used in sustainable systems, with were in comparison to the control (no fertilizers and manure applied) that selection in three systems. The experiment was conducted using a randomized complete blocks design with three replication. The physiological growth indices, such as dry matter, Leaf area index, and relative growth rate were determined. Dry matter and leaf area index in the intermediate system "20 tonha -1 of manure mixed with N=80, P=64 and K=80 kgha-1 of chemical fertilizers" pointed a noticeable increase during plant growth, compared to the methods. Seed yield increased %93.2, %14.1 and %8.6 related to control, chemical and organic systems respectively. In seed, the essential oil was %3.18 that increased %22.8 related to control and chemical system respectively and %10.8 related to organic systems. In the essential oil, anethole increased. Application of intermediate system improved soil physical, chemical and biologica properties and raised absorption of nutrient, plant canopy and light interception in agroecosystes.