To investigate the effect of nonuniform axial heat flux distribution and uneven radial heating and inlet throttling on density wave oscillations in reactors, RELAP5/MOD4.0 code is applied to conduct numerical simulations of a parallel channel system in forced circulation loops. The results obtained from the combination of non-homogeneous non-equilibrium model and semi-implicit numerical method in the code agree well with experimental data. Flow instability boundaries of linear and cosine axial heat flux distribution are compared and integral of axial heat flux along the channel is plotted to analyze the detailed mechanism. Besides, the critical phase change numbers of system and each channel under different nonuniformity of radial heating and inlet throttling are calculated. The results show that the system stability depends on the location of boiling boundary and the integral of axial heat flux along channel. Increasing or decreasing axial heat flux linearly has stabilizing or destabilizing effect compared with uniform axial heat flux respectively. Cosine heat flux increases system stability at low inlet subcooling. However, system stability could either be strengthened or weakened at high inlet subcooling. Inlet-peaked heat flux decreases system stability while outlet-peaked heat flux increases system stability compared with cosine heat flux. The influence of uneven radial heating on system stability is not significant. System stability decreases with nonuniformity of radial inlet throttling and it increases if the inlet throttling of one channel is increased.