The thermally induced phase transition of the poly(N-isopropylacrylamide) (PNIPAM) brush covalently bound to the surface of the gold nanoparticles was studied using high-sensitivity microcalorimetry. Two types of PNIPAM monolayer protected clusters (MPCs) of gold nanoparticles were employed, denoted as the cumyl- and the cpa-PNIPAM MPCs, bearing either a phenylpropyl end group or a carboxyl end group on each PNIPAM chain, respectively. The PNIPAM chains of both MPCs exhibit two separate transition endotherms; i.e., the first transition with a sharp and narrow endothermic peak occurs at lower temperature, while the second one with a broader peak occurs at higher temperature. With increase of the MPC concentration, the transition temperature corresponding to the first peak only slightly changes but the second transition temperature strongly shifts to lower temperature. The calorimetric enthalpy change in the first transition is much smaller than that in the second transition. The ratio of the calorimetric enthalpy change to the van't Hoff enthalpy change indicates that in the first transition PNIPAM segments show much higher cooperativity than in the second one. The investigation of pH dependence of two-phase transitions further indicates the PNIPAM brush reveals two separate transitions even with a change in interchain/interparticle association. The observations are tentatively rationalized by assuming that the PNIPAM brush can be subdivided into two zones, the inner zone and the outer zone. In the inner zone, the PNIPAM segments are close to the gold surface, densely packed, less hydrated, and undergo the first transition. In the outer zone, on the other hand, the PNIPAM segments are looser and more hydrated, adopt a restricted random coil conformation, and show a phase transition, which is dependent on both concentration of MPC and the chemical nature of the end groups of the PNIPAM chains. Aggregation of the particles, which may also affect the phase transition, is briefly discussed.