Abstract Supercritical water-cooled reactor (SCWR), which is considered as the logical extension of existing light water reactors (LWRs) (pressurized water reactor and boiling water reactor (BWR)), has the potential of increasing the efficiency of power generation to 45% compared to 33% of that of LWRs. But without the challenges of heat transfer and hydrodynamics, and reactor core design materials due to supercritical flow instability which is associated with sharp variation in fluid properties near the vicinity of the pseudo-critical temperature. Supercritical flow instability therefore needs to be addressed ahead of the deployment and operation of SCWR in the near future. The main purpose of this study is to carry out flow instability analysis in parallel channels with supercritical water. The study also aims at examining the capability of using three-dimensional (3D) simulation of turbulent flow in arbitrary regions computational continuum mechanics C++ based code (3D STAR-CCM+ CFD code) to predict flow oscillation amplitude and periods, and instability power boundaries at low-power boundary (LPB) and at high-power boundary (HPB). Parameters considered in the investigation include mass flowrate, system pressure, and gravity. Two different threshold power instability boundaries were obtained from the study. These instability power boundaries include lower threshold where stability of the parallel channel system decreases with increasing coolant inlet temperature, and upper threshold where stability of the parallel channel system increases with increasing coolant inlet temperature. From the results of the investigation, it can be found that: (1) for LPB at 23 MPa, only lower threshold was obtained as flow instability power boundary; and for HPB at 23 MPa, both lower and upper thresholds were obtained as flow instability power boundaries. The numerical findings quite well agree with the experimental findings at 23 MPa for both LPB and HPB; (2) only lower threshold was obtained as flow instability power boundary at both 23 MPa and 25 MPa for LPB. For HPB, both lower and upper thresholds were obtained as flow instability power boundaries at both 23 MPa and 25 MPa; (3) only lower threshold was obtained as flow instability power boundary for the parallel channel system with or without gravity influence for LPB. For HPB, both lower and upper threshold flow instability power boundaries were obtained for the parallel channel system with gravity influence, but only lower threshold flow instability power boundary was obtained for system without gravity influence; (4) only lower threshold was obtained as flow instability power boundary at system mass flowrates of 125 kg/h and 145 kg/h for LPB. For HPB, both lower and upper threshold flow instability power boundaries were obtained for system mass flowrate of 125 kg/h, but only lower threshold flow instability power boundary was obtained for system mass flowrate of 145 kg/h. For both LPB and HPB, the numerical findings agree quite well with the experimental results for a system operated at 125 kg/h and 145 kg/h; (5) the investigated parameters such as mass flowrate, pressure, and gravity have significant effects on amplitude of mass flow oscillation, but have little effects on the period of mass flow oscillation for both LPB and HPB. Results from the numerical simulation were compared with the results from the experiment for both LPB and HPB. The numerical amplitude results obtained were far less than the amplitude results obtained from the experiment. But there was no significant difference between the oscillation periods obtained from both the numerical simulation and experiment. (6) Flow instability studies including predicting flow oscillation amplitude and periods, and instability power boundaries could be carried out using 3D STAR-CCM+ CFD code. The effects of heating structures on flow instability results have not been considered in this study. Previous studies have shown that including heating structures in geometrical models for numerical studies may have effects on flow instability results. More experimental studies are needed for validation of similar numerical studies carried out at supercritical pressures using various numerical tools.