Using the second national economic census micro data with a multi-level model to overcome the productivity relevance of enterprises in city-level and industry-level, this paper estimates the production function with skill advantage bias, and also does a deep heterogeneous analysis. From the result, we find that, the increase in the proportion of high-skilled labor in service companies has a significant positive effect on the value-added creation ability of enterprises on the whole. On average, the ability of high-skilled labor to create added value relative to low-skilled labor is 1.218 times. Through further heterogeneous analysis, this paper finds that, compared with low-skilled enterprises, high-skilled enterprises can obtain higher value-added returns by increasing the proportion of high-skilled labor, and the skill- advantage of high-skilled labor in high-skilled enterprises is larger; Companies with the life service industry, the production service companies have higher value-added returns by increasing the proportion of high-skilled labor. At the same time, the production service companies have lager skill-advantage of high-skilled labor. In the sub-industries, the increase in the proportion of high-skilled labor in industries such as science technology, information technology, leasing and commerce has a significant positive effect on the value-added of enterprises; but in the industries such as retail, transportation, and accommodation and catering, the increase in the proportion of high-skilled labor has no effect or even negative effect on the added value of enterprises.