Hello Yukui,
could you please provide some more details on the behavior you are observing? Which species are you looking at? How many days have you simulated, and does the relative magnitude of the IC tag vs. the source region tags change over time? Does the IC tag have the same magnitude as the sum of the region tags or are all tags (region tags and IC tag) identical? Does the behavior of the BC tag look reasonable?
As noted in other forum posts discussing ISAM (e.g. here and here), we want to make sure you are aware of this Known Issue with CMAQ-ISAMv5.3.1 predictions of secondary gas species. A bugfix release (v5.3.2) is expected soon that will address this issue.