Urea is a widely applied fertilizer to enhance crop yields. Ecological risks associated with the excessive application of urea fertilizer threaten the paddy fields' sustainable agriculture and biodiversity preservation. There are no practical thresholds based on proven data on microbial communities. Protozoa are nitrogen-sensitive organisms. For the first time, this study conducted acute and chronic urea toxicity tests on eight species of organisms. The results indicate that Blepharisma sp. is the most sensitive species to urea exposure and is a suitable indicator for determining the safe threshold of urea. This study estimated the predicted no-effect concentration using species sensitivity distribution curves. Subsequently, it established the threshold for urea application in rice fields based on the fields' area and the surface water's height. The short-term safety threshold for urea in the studied paddy field with black soil is 87.7mg/L, equivalent to 43.85kg of urea per hectare for a single nitrogen fertilizer application. The long-term safety threshold is 5.02mg/L, representing the concentration for re-applicating urea. The biodiversity-safeguarding application threshold provides the basis for developing a urea fertilizer reduction protocol to safeguard the paddy fields' biodiversity.