<p>The large-scale development of China’s dairy farming has caused enormous pressure on the ecological environment. Due to the limitations of environmental regulations, this study attempts to explore the issue of waste disposal in dairy farms from the perspective of the supply chain structure. First, classify the supply chain structure in dairy sector (Integration form, Cooperative form, Contract form) and elaborate on the characteristics of each structure form. Furthermore, based on government recommendations for dairy farming technology, we quantify the level of waste disposal. Third, we use the ordered logit model to empirically analyze the impact of the supply chain structure on the waste disposal behavior. The conclusion is that the probability of implementing waste disposal through integration form is higher than that through cooperative form and contract form. The ranking of the probability of implementing waste disposal behavior is: integration form &gt; contract form &gt; cooperative form. After robustness testing, the results are consistent with the benchmark model, proving that the results are reliable. There is an “inverted U” shaped relationship between the scale and the waste disposal of dairy farms, the inflection points of scale calculated at 433 heads. In addition, cultivated area used for waste disposal, education level, waste pollution awareness, regulations, breeding area and other factors also significantly affect the waste disposal behavior of dairy farms. These conclusions can not only provide decision-making references for China, but also provide some references for other governments to formulate waste management policies for the dairy sector.</p>