A nanoparticle manufacturing system, comprising: an ablation chamber, having a transparent window on the top thereof; a substrate, being disposed in the ablation chamber for a target being put thereon; a cooling liquid inputting device, being connected to the ablation chamber via a cooling liquid transmitting tube, and used for inputting a cooling liquid to the ablation chamber; wherein a liquid surface height of the cooling liquid is controlled to be apart from a disposing height of the transparent window by a first distance, moreover, the liquid surface height being apart from the surface of the target with a second distance; a laser source for providing a laser beam; at least one light guide tube, having a light guidance-in end connected to the laser source and a light guidance-out end, wherein the light guidance-out end is extended into the ablation chamber for being apart from the surface of the target with a third distance; wherein the guidance-out end is lower than the liquid surface height of the cooling liquid; and a liquid surface controlling device, being connected to the ablation chamber and used for detecting the liquid surface height; therefore, by way of filling the cooling liquid into the ablation chamber and pumping the cooling liquid out of the ablation chamber, the liquid surface controlling device being able to control the liquid surface height to be apart from the disposing height of the transparent window with the first distance; wherein the laser beam emitted by the laser source is guided into the ablation chamber through the at least one light guide tube, so as to process the target to a plurality of nanoparticles. an ablation chamber, having a transparent window on the top thereof; a substrate, being disposed in the ablation chamber for a target being put thereon; a cooling liquid inputting device, being connected to the ablation chamber via a cooling liquid transmitting tube, and used for inputting a cooling liquid to the ablation chamber; wherein a liquid surface height of the cooling liquid is controlled to be apart from a disposing height of the transparent window by a first distance, moreover, the liquid surface height being apart from the surface of the target with a second distance; a laser source for providing a laser beam; at least one light guide tube, having a light guidance-in end connected to the laser source and a light guidance-out end, wherein the light guidance-out end is extended into the ablation chamber for being apart from the surface of the target with a third distance; wherein the guidance-out end is lower than the liquid surface height of the cooling liquid; and a liquid surface controlling device, being connected to the ablation chamber and used for detecting the liquid surface height; therefore, by way of filling the cooling liquid into the ablation chamber and pumping the cooling liquid out of the ablation chamber, the liquid surface controlling device being able to control the liquid surface height to be apart from the disposing height of the transparent window with the first distance; wherein the laser beam emitted by the laser source is guided into the ablation chamber through the at least one light guide tube, so as to process the target to a plurality of nanoparticles.