We present the results of global three-dimensional radiation magnetohydrodynamic simulations of the formation of soft X-ray emitting regions in active galactic nuclei by applying a radiation magnetohydrodynamic code based on the M1-closure scheme. The effect of Compton cooling is taken into account. When the surface density of the accretion flow exceeds the upper limit of the radiatively inefficient accretion flow (RIAF), the optically thin, hot accretion flow near the black hole co-exists with the soft X-ray emitting, warm (T = 106 – 107 K) Comptonized region around r = 20 – 40rs, where rs is the Schwarzschild radius. Numerical results indicate that when the accretion rate approaches the Eddington accretion rate, the warm Comptonized region stays in optically thin for effective optical depth, Thomson thick, and radiation pressure dominant state. This region is found to oscillate between a geometrically thin, cool state and a geometrically thick state inflated by radiation pressure. The time variability of the accretion flow is consistent with that of the narrow-line Seyfert 1 galaxies.