A crystal oscillator and manufacturing method thereof are provided. The crystal oscillator includes: a semiconductor substrate; an interlayer dielectric layer located on the surface of the semiconductor substrate, an excitation plate and a positive electrode plug and a negative electrode plug being formed inside the interlayer dielectric layer, and the positive electrode plug and the negative electrode plug being located at the both sides of the excitation plate; a bottom cavity on top of the excitation plate, located between the positive electrode plug and the negative electrode plug; a vibrating crystal located on the surface of the interlayer dielectric layer, across the bottom cavity and connected with the positive electrode plug and the negative plug, wherein the vibrating crystal connects the positive electrode plug and the negative electrode plug at its both sides and besides the other both sides are the free ends and do not contact with the surrounding objects; an isolating layer located on top of the interlayer dielectric layer, a gap between the isolating layer and the vibrating crystal thus forming a top cavity; a covering layer formed on the surface of the isolating layer. The crystal oscillator is manufactured based on Complementary Metal-Oxide-Semiconductor Transistor (CMOS) technology, and can be integrated into the semiconductor chip easily and can meet the requirement for the miniature components.