Natural organic fertilizer (NOF) as a kind of rural garbage waste, it has been used as an soil amendment to improve fertility and crop yield. However, the effects of NOF of fertility on loess soil have not been thoroughly investigated. To provide a scientific basis for establishing a reasonable fertilization model, this paper evaluated the effect of adding organic fertilizer on fertility different soil. Three different loess soils were used as the research object, and sixteen indicators such as pH values, soil organic carbon (SOM), ammonium nitrogen (AN), available phosphorus (AP), available potassium (AK), exchangeable calcium (ECa) etc. were evaluated to assess the effect of NOF addition on the fertility of different types of soil. The three groups (sheep manure, chemical fertilizer, sheep manure combine with chemical fertilizer) of soil fertility were analyzed through a one-years field experiment. The results showed that SOM, AN, AP and AK were improved by adding NOF. Correlation analysis showed that SOM was significantly correlated with nitrate nitrogen (NN), AK and ECa. Principal component analysis (PCA) and cluster analysis (CA) were used to assess fertility in different types of loess soils. The PCA results showed that the first principal component (PC1) consisted of pH, AN, NN, AK, etc., and the second principal component (PC2) contained SOM, AP, ECa, ACu and ACl. In the thrid principal component (PC3), however, ASi and available boron (AB) accounted for only 19.8%. The cluster analysis (CA) used was comparable and the results showed that the order of increasing soil fertility levels was. Loessal soil > Sierozem > Dark loessal soil. In conclusion, these results suggested that NOF used in combination with inorganic fertilizer can significantly improve soil fertility and regulate soil nutrient balance in loess soils, at the same time, NOF improved soil fertility and realized the reuse of solid waste, which is of great significance to the environment and ecological tourism.