Emotional communication is part of our life. However, it is not easy for humans to understand each other’s feelings. Computer-mediated communication (CMC) technologies can help us with emotional communication. However, when we are having a misunderstanding or expressing our emotion, it arises the doubt that the receivers can receive the correct emotion of senders. Since expressed emotion can be arbitrarily changed, they can be said to lack objectivity, which is necessary for emotion estimation. There is a method of emotional analysis using biological signals such as heartbeat and brain waves has been studied. Biological information cannot be changed arbitrarily, therefore can be said to be objective, meaning more suitable for unconscious emotion estimation on CMC context. In this paper, we describe our experiment of comparison of the unconscious emotion that is estimated by bio-estimated emotion method, with the conscious feeling at the communication of CMC. The results show that unconscious emotion obtain the lowest evaluation. Also, the unconscious emotion obtains the highest evaluation at using the self-understanding. In this paper, we describe the experimental process and results in detail, and discuss the results and future research directions.