In rural toilets, black water still remains polluted by nitrogen and phosphorus after being pre-treated by septic tanks. This study uses aerated biofilters to purify black water, screen the biofilter filler, and determine its effect on nitrogen and phosphorus purification in rural black water. This study introduced the concept of the “shape factor” into the Langmuir and Freundlich equations and optimized the isotherm adsorption model to better fit the actual dynamics of nitrogen and purification in black water. Combined with the first-order kinetic equation, the double constant equation, and the Elovich equation, the adsorption performance of seven kinds of biofilter fillers (i.e., zeolite, volcanic rock, sepiolite, ceramsite, anthracite, vermiculite, and peat) was studied. Then, the biofilter was constructed using a combination of fillers with better adsorption properties, and its ability to purify rural black water was studied. Results showed that vermiculite and zeolite had little effect on nitrogen and a high saturated adsorption of 654.50 and 300.89 mg·kg−1, respectively; peat and ceramsite had little effect on phosphorus and a high saturated adsorption of 282.41 mg·kg−1 and 233.89 mg·kg−1, respectively. The adsorption rate of nitrogen from fast to slow was vermiculite > peat > zeolite > volcanic rock > sepiolite > ceramsite > anthracite. The adsorption rate of phosphorus from fast to slow was peat > ceramsite > zeolite > sepiolite > vermiculite > volcanic rock > anthracite. Four combined biological filter fillers aided the removal of nitrogen and phosphorus from rural high-concentration black water. The combination of zeolite and ceramsite filler had a good nitrogen and phosphorus removal effect in high-concentration black water. After the system was stable, the nitrogen removal rate attained 71–73%, and the phosphorus removal rate attained 73–76% under the influent condition of total nitrogen and phosphorus concentrations of 150–162 and 10–14 mg·L−1, respectively. This study provides technical support and reference for the purification and treatment of rural black water.