Based on Potsdam Magnetic Model of the Earth (POMME6.2), the spatial distribution of crustal magnetic anomalies around eastern Himalayan syntaxis and their decay with altitude were studied. The two-dimensional wavelet transform method was employed to decompose ground magnetic anomalies and analyze combination of wavelet details and anomalies of approximation signal. The relationship between magnetic anomaly and geological structure was discussed. The results show that the distribution of crustal magnetic anomalies over the study area is considerably non-uniform. Relatively strong negative magnetic anomalies were distributed over Himalaya-Eastern syntaxis-Longmen mountains-Daba mountains, whereas positive magnetic anomaly is present over Sichuan Basin, with weaker magnetic anomalies over other regions. The eastern syntaxis had important impact on magnetic anomalies around. All crustal magnetic anomalies over eastern syntaxis and the surrounding regions were medium- and short-wavelength positive/negative ones superposed onto a negative or weak magnetic anomaly setting. These meso- and micro-scale magnetic anomalies were generated from magnetic materials in the upper and middle crust, with strikes basically consistent with geological structures. Along Jinshajiang- Honghe Fault Belt, there is a sharp weak magnetic anomaly belt. Longmenshan Fault Belt, Lijiang-Xiaojinhe Fault Belt and Honghe Fault Belt are transitional zones between strong and weak magnetic anomalies. The east-west magnetic anomalies in the central Tibetan Plateau exhibited arc shape in the dome of Eastern Syntaxis. The banded lumpy magnetic anomalies over the central Tibetan Plateau and Central Yunnan massif had the same decay rule.