The degradation of composite mesoporous silica nanoparticles is quite important for the in vivo use of this delivery carrier. We investigated the dynamic silica degradation of core–shell structured magnetic mesoporous silica nanoparticles (M-MSNs) and its counterpart with polyethyleneimine coating (M-MSN@PEI) in PBS. It is confirmed for the first time that M-MSNs unexpectedly experienced a preferential dissolution from the inside part of the mesoporous shell, leading to a rattle-type degradation structure. Additionally, the presence of polyethylenimine (PEI) can maintain this transition state of rattle-type structure for more than 50 h of immersion in PBS, whereas the same structure was disintegrated after 2 h for bare M-MSNs. We then tried to put forward a possible degradation mechanism for this type of core–shell M-MSNs by studying and comparing with the dissolution behaviour of pristine mesoporous silica nanoparticles (MSNs). It is discovered that two pivotal factors governed this unique process: (a) the unique shell structure with lower interior pore order and (b) the role of PEI chains in affecting silicate condensation. There is no doubt that the present study will provide guidance for the design and in vivo bio-applications of an M-MSN-based delivery system.