In 2009 the former three surveys on small and medium enterprises were combined into one survey to reduce the response burden of enterprises. In this report, we study a sample design for 2009 survey on actual state of small and medium enterprises (SMEs). However, the differences between the manufacturing industries and knowledge-based service industries are so large that we need to consider separate populations in the survey. The total sample size is decided as 10,000 in new survey design for integration. We allocate the sample sizes for the first stratum based on CV and then allocate the sample sizes for the second stratum using root proportional formula. Also we calculate survey weights and propose the formula for the estimators as well as standard errors using weights for each characteristic.