The present analysis is aimed at conducting node sensitivity analysis on the thermal–hydraulic performance of supercritical fluid in a three parallel channel configuration system. The heated channel was divided into different nodes and is examined under wide-ranging operating conditions. Firstly, the heated channel was divided into two nodes, like the two-phase flow system. In the second case, based on the correlation between the fluid properties, the heated channel was divided into three regions: heavy, mixture, and supercritical fluids. Finally, the channel was divided into N-nodes. Post the nodalization analysis, a non-linear analysis of three parallel channels was carried out under varied heat flux conditions. The analytical approximation functions were developed to capture the fluid flow dynamics. These functions were used to capture each node’s density, enthalpy, and velocity profiles under a wide range of operating conditions. The different flow instability (density wave oscillations and static) characteristics were observed at low pseudo- and relatively high subcooling numbers. In the density wave oscillations regime, out-of-phase oscillations and limit cycles are observed. A co-dimension parametric analysis with numerical simulations was carried out to confirm the obtained non-linear characteristics. Such analysis for parallel channel systems under supercritical working fluid flow conditions is missing in the literature which is limited to only linear stability analysis. This analysis can help to improve heat and mass transfer for designing efficient heated channel systems.