A light-emitting diode (LED) chip structure with a cup-like reflective element is provided. The LED chip structure comprises a substrate, an isolation element and a mesa including an LED surrounded by the isolation element. The isolation element comprises an upper isolation part and a lower isolation part. The lower isolation part is positioned in the substrate and the upper isolation part protrudes from a surface of the substrate. A reflective layer is disposed on a sidewall of the upper isolation part, and a bottom of the reflective layer does not contact the mesa. The cup-like reflective element at least includes the isolation element with the reflective layer.