As the first pilot site of the Globally Important Agricultural Heritage System (GIAHS), Qingtian rice-fish co-culture system has attracted more and more attention due to its unique advantages. In order to better conserve the first GIAHS project in Asia, we investigated the effects of different rice planting densities on soil fertility of Qingtian rice-fish co-culture systems. The results showed that the pH value of the tested paddy soil varied between 5.50-6.13, which was weakly acidic. The contents of soil nutrients (such as the soil total nitrogen, soil organic matter, available phosphorus and available potassium) first decreased and reached the lowest values at the booting stage, then recovered to the similar higher levels with the initial before rice harvesting, indicating that the activity of the field fish and perhaps fish feces could help maintain the soil fertility. According to the results of Grey relational analysis (GRA) between rice yield and soil nutrient, it was found that soil pH and available potassium were most closely related to rice yield. Compared with the rich nitrogen, available phosphorus and soil organic matter, the less suficiently available potassium and low pH value might be responsible for the limited growth and yield of rice. Rice planting densities were not found to significantly affect soil fertility in Qingtian rice-fish co-culture system in this growing season.