We discuss the specific risk significance in the extended pre-defueled phase on the basis of the refueling mode operation of BWR-4 in the decommissioning process, especially under the condition that all spent fuels are still in core. The incorporative influences of the reactor core and the spent fuel pool (SFP) are investigated, and the methodology is systematically developed via the two primary configurations including sensitive studies. One is the movable refueling gate between the reactor core and SFP, and the other is the residual heat removal (RHR) system. The decay heat levels after shutdown and the success criteria are analyzed by means of a realistic thermal-hydraulic code, MELCOR. In this study, 30-days after permanent shutdown is chosen and consequently two configurations can be defined, respectively. Under the situation of decreasing decay heats after shutdown and long time available for human actions, two operator tasks are assumed to be independent. Furthermore, the WinNUPRA software package is used for the fuel damage sequence quantification. The relevant initiating events are shown, including: Flow diversion LOCA, LOCAs in connected systems, Loss of offsite power (LOOP), Loss of coolant accident (LOCA), Loss of cooling, Test and maintenance induced LOCAs, etc. The significant risk contributors account for more than 90% of the total fuel damage frequency (FDF). The quantification results for the FDF realistically show that the Basic configuration (gate open) is two orders of magnitude (2%) lower than the Sensitivity configuration (gate closed) as a result of human action dependence and cooling systems (RHR and spent fuel pool additional cooling system (SFPACS)).