Cropping systems in farmland areas of Iran are characterized by continuous cultivation of crops with consumption of chemical fertilizers leading to serious soil erosion and fertility decline. Information regarding the simultaneous evaluation of crop rotation and fertilization on the canola traits is not available. Therefore, an experiment was conducted during 2007 - 2010. Experimental designs were arranged in a split plot based on randomized complete block design with three replications. Main plots were consisted of three crop rotations and sub plots were consisted of six methods of fertilization. Results showed that the activities of all soil enzymes were generally higher in the organic manure (compost + farmyard manure) treatment. The highest grain nitrogen (34.2 mg/g), sulfur content (4.43 mg/g) and the lowest N/S were obtained in the green-manured rotation. The highest grain N (38.9 mg/g) was obtained in co application of chemical and organic manure treatment. Grain yield in green-manured rotation and co application of chemical and organic manure treatment were higher than other treatments. Canola-wheat-canola rotation had lower oil content and oil yield than those of other rotations. The highest percentage of oil was obtained from farmyard manure and compost application and the highest oil yield belonged to combined application of chemical and organic fertilizers treatment. Application of organic manure significantly increased unsaturated fatty acids.