As far as we known, recent studies on the origin of agricultural products rarely focus on the source of cities or counties even small-scale districts, but traceability of small-scale districts of food is the research trend and difficulty of future researches. The most commonly used methods of origin tracing researches are stable isotope and element technology, because these indicators are directly related to local geographical environment. However, when the region of traceability is very close, it is necessary to find new parameters to enhance the accuracy of traceability in small-scale districts. This study uses a combination of nutritional (amino acids) and geographical parameters (stable isotopes, elements) to trace the origin of milk from eleven districts located in five cities of Inner Mongolia. The results showed that the combination of nutritional (amino acids) and geographical parameters (stable isotopes, elements) was the best source tracing method.