A photothermal deflection measuring system includes a substrate, a detecting light source, a detecting unit, and a processor. The substrate includes a plurality of positioning structures, on each of which supports a cell emitting heat outside a surface thereof. The detecting light source is utilized to project a detecting light passing through a specific position outside the surface whereby the detecting light is deflected due to a thermal gradient caused by the emitted heat. The detecting unit is arranged at a side of the cell for receiving the deflected detecting light thereby generating an optical deflection signal corresponding to a deflection of the deflected detecting light. The processor is configured to receive the optical deflection signal, analyze the optical deflection signal and determine a heat value corresponding to the specific position out side the surface of the cell according to the optical deflection signal.