Organic fertilizer is increasingly valued in the process of agricultural development. It can improve and enhance soil fertility while promoting high-quality and efficient crop production. It contains rich organic and inorganic nutrients and plays an irreplaceable role in reducing fertilizer application. The data set included the content of organic fertilizer raw materials and heavy metals in commercial organic fertilizer in Inner Mongolia. In the eastern and western parts of Inner Mongolia, 116 fertilizer samples(including chicken manure and sheep manure), 74 organic fertilizer raw materials and 42 commercial organic fertilizer samples were be collected. Sheep manure, cow manure and chicken manure of organic fertilizer raw materials were all be detected. One sheep manure sample contained 373.2 mg/kg lead which is exceed standard. The commercial organic fertilizer were all be detected heavy metals but not exceed standard. The content of heavy metals in commercial organic fertilizer was higher than raw material except zinc. The content of heavy metals in sheep manure was higher than that in the mixture of sheep manure and cow manure. Inner Mongolia organic fertilizer raw materials, commercial organic fertilizer overall situation is preferably.