This study aims to identify the rhythmic measures that present challenges for L2 Chinese learners and whether these challenges are more unique for learners with specific L1 backgrounds. Also, we analyzed the role of these rhythm features in assessing the perceived naturalness of L2 Chinese speech. 107 L2 Chinese learners from five L1 backgrounds, including Vietnamese, Japanese, Thai, Russian, and Korean, were recruited to elicit L2 speech using an identical reading task. Perceived naturalness was evaluated based on the subjective judgment of six Chinese native speakers. Linear discriminant analysis, combined with linear model analysis, showed that consonant-related measures (VarcoC, nPVI-C, ΔC, rPVI-C) were better indices for classifying L2 Chinese rhythm by five L1-background groups, indicating L1 influence on L2 rhythm. However, the effect of consonant-related measures was mainly demonstrated in Japanese and Russian learner groups. Vowel-related rhythm measures (ΔV, VarcoV, rPVI-V, nPVI-V) showed a tendency toward universal constraints, as all L2 groups manifested mastery in the rate-normalized variability of vowel duration (VarcoV, nPVI-V) and the deficiency in the raw indices (ΔV, rPVI-V). Linear regression analysis also revealed that vowel duration (meanV) and the complexity of consonants (ΔC) contributed to the perceived impression of naturalness in L2 Chinese.