The purpose of this study is to investigate the understanding of middle school students on the meaning of proof and to suggest a teaching method to improve their understanding based on three levels identified by Kunimune as follows: Level I to think that experimental method is enough for justifying proof, Level II to think that deductive method is necessary for justifying proof, Level III to understand the meaning of deductive system. The conclusions of this study are as follows: First, only 13% of 8th graders and 22% of 9th graders are on level II. Second, although about 50% students understand the meaning of hypothesis, conclusion, and proof, they can`t understand the necessity of deductive proof. This conclusion implies that the necessity of deductive proof needs to be taught to the middle school students. One of the teaching methods on the necessity of proof is to compare the nature of experimental method and deductive proof method by providing their weak and strong points respectively.