A multilevel clean energy heating system comprises a water source circulating pump, a water source heat pump main unit, a hot water circulating pump, a hot water warmth-retaining tank, a first hot water supply pump, a natural gas stove, a solar water heating system, a second hot water supply pump, a solar hot water warmth-retaining tank and a third hot water supply pump. The water source heat pump main unit is connected with a tap water incoming pipe of the water source circulating pump through a pipeline. The water source heat pump main unit includes a direct heat pump, a low temperature retention tank, and a circulating heat pump. The direct heat pump is connected with the tap water incoming pipe of the water source circulating pump through a pipeline. The direct heat pump is connected with the low temperature retention tank through a pipeline. The low temperature retention tank is connected with the circulating heat pump through a pipeline.