The embodiment of the invention discloses a photodiode and a manufacturing method thereof, relating to the field of opto-electrical technology, wherein the photodiode is capable of reducing the energy loss. The photodiode comprises a substrate positioned on a bottom layer, a lower cladding layer boss covering the substrate, an incident wave core guiding layer covering the lower cladding layer boss, an upper cladding layer covering the incident wave core guiding layer, an optical matching layer positioned above the upper cladding layer and an avalanche photodiode positioned above the middle part of the back end of the optical matching layer, wherein the width of the lower cladding layer boss at the tail end in the incident wave direction is wider than that of the beginning end in the incident wave direction, both sides of the lower cladding layer boss at the tail end in the incident wave direction are parallel, and both sides of the lower cladding layer boss at the beginning end in the incident wave direction are parallel; and the optical matching layer comprises an optical matching layer front end and an optical matching layer back end, wherein the optical matching layer front end comprises at least one air seam extended along the incident wave direction, and the optical matching layer front end is divided into characteristic units partitioned by the air seams. The embodiment of the invention is applied to manufacturing the photodiode.