Previous studies on L2 (i.e., second language) Chinese compound processing have focused on the relative efficiency of two routes: holistic processing versus combinatorial processing. However, it is still unclear whether Chinese compounds are processed with multilevel representations among L2 learners due to the hierarchical structure of the characters. Therefore, taking a multivariate approach, the present study evaluated the relative influence and importance of different grain sizes of lexical information in an L2 Chinese two-character compound decision task. Results of supervised component generalized linear regression models with random forests analysis revealed that the orthographic, phonological and semantic information all contributed to L2 compound processing, but the L2 learners used more orthographic processing strategies and fewer phonological processing strategies compared to the native speakers. Specifically, the orthographic information was activated at the whole-word, the character and the radical levels in orthographic processing, and the phonological information at the whole-word, the syllable, and the phoneme levels all exerted contributions in phonological processing. Furthermore, the semantic information of the whole words and the constituents was accessed in semantic processing. These findings together suggest that the L2 learners are able to use cues at all levels simultaneously to process Chinese compound words, supporting a multi-route model with a hierarchical morphological structure in such processing.