The evaluation of fertility of agricultural soils should not only include the chemical properties but also biological properties. A simple and rapid evaluation method of soil fertility is proposed (soil fertility index; SOFIX) based on bacterial biomass, nutrient circulation activities, and chemical properties. Methods for estimating bacterial biomass, nitrogen circulation activity, and phosphorus circulation activity are developed. Using the new methods, a SOFIX database of upland agricultural fields is constructed. Based on the SOFIX database, methods for the enhancement of material circulation are also developed for an efficient organic agricultural system.