Recently, confinement of polymers with different geometries has become a research hotspot. Here, we report the dramatic deviation of glass transition behaviors of poly(methyl methacrylate) (PMMA) confined in cylindrical nanopores with diameter significantly larger than chain's radius of gyration (R-g. Fast cooling a PMMA melt in the nanopores results in a glass with one single glass transition temperature (T-g). But two distinct T(g)s are detected after slow cooling the melt. The deviation in T-g could be as large as 45 K. This phenomenon is interpreted by a two-layer model. During vitrification under slow cooling two distinct layers are formed: a strongly constrained interfacial layer showing an increased T-g as compared to that of the bulk polymer and a core with a decreased T-g. By thermal annealing experiments, we find that these two T(g)s are inherently correlated. In addition, the deviation of T-g for PMMA confined in nanopores reveals a dependence on molecular weight.