As a major cause of non-native accent for L2 learners, L2 intonation plays an important role in the acquisition of L2 suprasegment. Few studies have been on the prosodic encoding of Chinese intonation by Uygur learners with Mandarin Chinese as a second language (CSL). With L2 Intonation Learning theory (LILt) as the theoretical framework, this study investigates the prosodic encoding of Mandarin intonation by Uygur CSL learners and compares with Beijing Mandarin speakers. Twelve speakers were invited to produce six pairs of Mandarin declarative and interrogative intonations in different tone sequences. It is found that for Uygur CSL learners, the pitch is falling in Mandarin declarative intonation and rising in interrogative intonation, which is similar to Mandarin speakers. However, the bottom lines in two intonations both drop slower. The interactions of L1 and L2 result in the narrowing trend of tonal pitch ranges (TPRs) in declarative intonation assimilated to L1 and the expanding trend in interrogative intonation assimilated to L2.