The method of Six Sigma has been implemented popularly in some industries worldwide and created great values to the enterprises. One of key tools of six sigma ”Throughput Yield” which used in the define phase provides a simple way to estimate the performance of processes and (or) focus the problem of manufacturing. However, there still are some hidden problems, which are not easy to be figured out, and these may lead the six sigma project to make a mistake on focusing the wrong process or wrong project chosen. This paper discussed the problems when implementing six sigma with the tool ”Throughput Yield” in the define phase. Followings are the description of problems. The first, which formula we should use? The second, how does the impact of throughput yield estimation? The third, how does the impact of demerits classified and weighted in the throughput yield analysis? The fourth, how does the effect of cost on the throughput yield analysis? We discussed all above problems. Furthermore, we provide some feasible solutions to the Six Sigma Teams for reference.