Abstract: Aerobic composting is one of the most effective technologies for the harmless treatment and resource utilization of cow manure in recent years. Effective disposal of cow manure is very necessary for the growth of soil and crops, together with human health, due to the large number of bacteria, viruses, and eggs of pathogenic parasites. In addition, some dairy manure is used as cow mattress materials after aerobic composting. If the pathogenic bacteria cannot be completely killed, some diseases (such as mastitis) can pose a serious risk to dairy cows, even to the yield and quality of milk. Among them, the National standard of Technical Specification for Composting Livestock and Poultry Manure releases that the stack temperature should reach above 55℃ and the maintenance time should not be less than 15 d, while the tank composting time should not be less than 7 d, and the reactor composting time should not be less than 5 d. The bottom ventilation is often used for aeration in the process of aerobic composting. At the same time, the stratification can be caused by the different materials at various levels of the reactor, as the gas temperature and water vapor content change with the air entering. The stratification phenomenon (such as dehydration) often existed in the aerobic composting process, damage to the uniformity and overall quality of the fermentation products. This study aims to explore the stratification of pathogen inactivation in aerobic composting materials. Three groups of experiments were set (T2 high temperature, T3 cooling, and T4 high temperature/cooling period turning), where non-turning (T1) was used as the control group. A systematic analysis was made of the conventional physical and chemical properties, as well as the pathogen removal efficiency during aerobic composting of cow manure. KRIGING method was utilized to interpolate the temperature and moisture content in different positions of the compost. The results showed that the fermentation temperatures under the four treatments reached above 55℃, fully meeting the requirements of the Technical Specifications for Composting Livestock and Poultry Manure Composting. Specifically, the peak temperatures were 71.35, 72.10, 70.20, and 70.25℃, respectively. The T3 and T4 treatments reached 7 days for the longest high-temperature period. The T4 treatment presented the highest removal rate (up to 97.15%) of the pathogen. Furthermore, the moisture content of the pile was from the high to the low in the order of the upper, middle, and lower layers. The removal efficiency of the pathogen was ranked in the descending order of the middle, lower, and upper layers in the aerobic composting materials. The pathogen removal rates were all higher than 80% in the four treatments. Consequently, the turning and throwing (T4 treatment) in the high temperature and cooling period is more conducive to the overall harmlessness of cow manure and stover mixed compost materials. This finding can provide technical guidance for the removal of pathogenic bacteria, in order to optimize the turning parameters in the aerobic composting of cow manure.