Disclosed urea microvia structure of a flexible circuit board and a manufacturing method thereof. A first through hole is formed in a first conductive layer of a flexible circuit board and a first exposed zone is defined. A second conductive layer includes a second through hole formed therein and defines a second exposed zone. A dielectric layer includes a dielectric layer through hole corresponding to the second through hole of the second conductive layer. A conductive paste layer is filled in the second through hole of the second conductive layer, the dielectric layer through hole of the dielectric layer, and the first through hole of the first conductive layer in such a way that the conductive paste layer covers and electrically contacts the first exposed zone of the first conductive layer and the second exposed zone of the second conductive layer.