Abstract: Marine heatwaves (MHWs) have become a frequently occurred extreme climate phenomenon in recent years and exert significant impacts on both ecological environment and social economy, thus attract great attentions from scientists. In this study, we utilize ocean heat content (OHC) to assess the short-term prediction skill of the First Institute of Oceanography-Climate Prediction System version 2.0 (FIO-CPS v2.0) on the MHWs in upper ocean, and further employ heat budget analysis to investigate intricacies of the MHW prediction. Our findings reveal that the prediction skill of FIO-CPS v2.0 on MHWs exhibits regional and seasonal variations. The prediction skill is better in tropical eastern and western Pacific, and northeastern Pacific. It is worth to note that in tropical eastern Pacific the prediction system encounters spring prediction barrier, but performs well in fall in tropical western Pacific and northeastern Pacific. Further analysis shows that the prediction skill is closely related to the underlying driving mechanism of the MHWs. In tropical eastern Pacific, the prediction skill of the MHWs come mainly from that of El Niño-Southern Oscillation (ENSO). In northeastern Pacific, the surface and subsurface prediction skills are attributed to surface heat flux and horizontal advection, respectively, while in tropical western Pacific the prediction skill is provided by vertical advection. Additionally, FIO-CPS v2.0 demonstrates the ability to predict the changing characteristics of the MHWs under global warming. This study not only promotes our understanding on the prediction skill of short-term climate prediction system FIO-CPS v2.0 but also offers a valuable reference for the short-term prediction of the MHWs in upper ocean.