In previous works, we introduced a new operational scheme named the passively autonomous frequency control operation (PAFO) to be applied in ATOM which is a soluble-boron-free (SBF) 450 MWth PWR. In PAFO, the control rods and soluble-boron are not utilized to vary the core power. Instead, the transients are entirely achieved by the passive response of the SBF core to the core inlet coolant temperature variation. The previous feasibility study was performed using a lumped PWR model. In this paper, we perform 3-D transient and thermal-hydraulic (TH) coupled neutronic simulations of PAFO in ATOM. The time-dependent TH model comprises core analysis for all fuel channels, particularly, by coupling fuel heating, heat transfer from the heated clad surface to the coolant, and single phase flow field. The flow field model solves the conservation equations of mass, energy, and axial momentum. The neutronic modeling is based on the typical two-step procedure for light water reactors. The various cross-sections and transient parameters are obtained using 3-D Monte Carlo simulations using Serpent-2 code with ENDF/B-VII7.1 data library. Meanwhile, two different options are implemented for obtaining the 3-D diffusion whole core solution using the nodal methods: the nodal expansion method and the semi-analytical nodal method. The neutronic and TH models of the reactor core are coupled with a steam generator model to simulate the impact of power demand variation on the core inlet coolant temperature. In addition, the predictor corrector quasi-static method was implemented to reduce the cost of the transient neutronic solution. The system models are solved using an in-house FORTRAN-95 code. This study is carried out for both primary and secondary frequency control operations at the beginning, middle, and end of the fuel cycle. Tolerable deviations of the axial shape index, 3-D power peaking factor and core coolant temperature during the passive power transients reflect good potential of the proposed PAFO scheme in ATOM.