Thermal stability investigations of photovoltaic structures synthesized by the compression plasma flow treatment of doped silicon are performed. The samples are annealed in an atmosphere of nitro gen, in air or in vacuum in a temperature range of 100-900°C for 30 min or 3 h. The photovoltaic effect does not change after annealing at temperatures up to 600-700°C. It decreases 1.3-1.7 times after thermal annealing at a temperature of 900°C. The structure-phase changes of silicon treated with compression plasma flows are studied using X ray diffraction and scanning electron microscopy methods. It is established that a recrystallized pre surface layer with a thickness of 10-20 μm and modified (but not melted) layer with a thickness of up to 50-60 μm localized below the recrystallized layer are formed.