Rational use of agricultural organic waste resources and scientific application of organic fertilizers (OFs) are of great significance to improve soil fertility and agricultural products quality and to reduce non-point source pollution. This paper reviews the possible risk factors and their hazards when organic fertilizer application. Heavy metals, antibiotics, environmental hormones and microplastics in OFs would result in risks of ecological contamination and agricultural product safety. The adverse effects of high salt content and insufficient maturity of OFs on crop growth. Biological safety risks such as OFs containing pathogenic organisms of plant, animal, and human. Attention should be paid on the risk of biological invasion from the imported OFs. The relevant limit indexes in OF standards were summarized.