Most previous studies on Chinese-Japanese bilingual lexical access have shown that cognates can facilitate L2 Japanese word recognition, and phonological overlap cannot. However, the findings from this research challenge those findings. In this study, both high- and low- proficient JFL (Japanese as a Foreign Language) learners performed phoneme monitoring tasks in their second language. Orthographically similar words with high or low phonological and semantic similarity were fully crossed. Our results suggest that phonological overlap across Chinese and Japanese interferes with phoneme processing speed and accuracy, especially those of the low-proficient JFL learners. Yet as their L2 proficiency improves, this inhibition effect can become smaller. In addition, cognate semantic overlap marginally interacts with L2 proficiency to affect phoneme recognition, though cognates do not directly play a role in phoneme processing. The theoretical implications of our research suggest that phonology functions as a non-selective element in the phonological access phase for bilinguals literate in two logographic languages. Moreover, cross-logographic processing does not conform to the cascading model; instead, it can be more accurately described by the modular or interactive models of bilingual processing.