Due to the safe, green, and sustainable features, organic farming systems have been received widespread concern in China and other countries. There are lots of the comparisons between organic and conventional farming systems since the organic farming system was developed, but systematic comparison based on the perspective of soil and fertilizer is little. Soil provides the direct living environment for plant, so based on the perspective of soil and fertilizer can fully understand the nature and influence of organic and conventional farming systems. In this paper, the previous research results were comprehensive analyzed about the comparison of organic and conventional farming systems based on the perspective of soil and fertilizer, and the difference and possible reasons of the crop yield, quality, soil fertility effects, environmental effects in the two farming systems were preliminary illustrated. Compared to the conventional farming system, the crop yield in organic farming system was lower at early stages, but it has great yield-increasing potential and organic farming system can improve soil properties and fertility, and generally improve crop quality, moreover, the pollution risks of atmospheric and water environment were lower in the organic farming system. The reasons for these differences may be the slowly release rate of the soil nitrogen and the available nutrients at the early stage of the organic farming system, and with the increase of the planting years, soil carbon sequestration capacity was gradually increased, soil microbial diversity was enhanced and soil nutrient utilization was improved.