The reuse of human excreta as biofertilizer resources offers a new option for meeting the growing demand for food and addressing the scarcity of soil productivity. Feces and black water are two prevalent forms of human excreta, both of which contain potentially harmful substances and therefore need to be treated in an environmentally sound manner by appropriate means. Ectopic fermentation bed systems (EFSs) seem to be a new technique for effective human excreta management and the production of biofertilizers using decomposed fillers. Therefore, the objective of this study was to evaluate and compare the nutrient content and fertilizer potential of decomposed fills after treatment of human feces and black water by an EFS under different application conditions. The results showed that the application of an appropriate proportion of fillers was beneficial to promote the growth of pakchoi, improve the yield and quality of pakchoi, and enhance soil fertility. The safe production requirements of agricultural products can be met as long as a reasonable filler application rate is maintained, with human feces fillers controlled within 5% and black water fillers controlled within 10%. The main factors affecting the yield and quality of pakchoi in this study were soil properties, especially soil EC. These findings help to better clarify the agronomic value of human excreta; however, the effects of long-term filler application need to be further explored.