Micro-CT technology and LA-ICP-MS were applied to studying the response relationship between carp otolith and heavy metals in waters. The LA-ICP-MS analysis has revealed that the contents of Cu and Pb of otoliths in Baiyangdian are higher than the contents of corresponding elements of otoliths in the Miyun reservoir, and the Micro-CT data show that the Micro-CT value of otolith from the Baiyangdian is higher than that from the Miyun Reservoir. The authors consider that the contents of Cu and Pb seem to be the main factors responsible for the difference of Micro-CT values of otolith from different waters.