The current study examined the process of learning Chinese character words in Chinese and Japanese of Chinese-native learners of the Japanese language. We estimated the learner’s learning process by examining the process of Chinese character words. We conducted 2 experiments while manipulating the degrees of orthographical and phonological similarities. Experiment 1 used a two by two factorial design with presentation language (first language, and second language) and orthographical similarity (high and low) , and Experiment 2 used a two by two factorial design with presentation language (First and second language) and phonological similarity (high and low). These experiments suggested the following; (1) Words with high orthographical similarity have similar processing both in the first and the second language regardless of the learner’s proficiency levels of the Japanese language, (2) learners with low proficiency had more active phonological representations of the native language that affected the processing of words, while learners with high proficiency had more active phonological representations of the second language that affected the processing of words. In learners of the Japanese language whose native language is Chinese, discrimination between the orthographical information of the Chinese and the Japanese languages was easy, while instant discrimination between the phonological information of the two languages was more difficult. The study elucidated that Chinese native speakers utilize both orthographical and phonological representations in their native Chinese language in learning Japanese kanji characters. The results indicate the importance of being keenly aware of the learning process where learners read Japanese kanji words using Chinese phonology.