A waterproof control unit is provided in which: connector housing is fixedly positioned onto circuit board that is mounted onto base; a first seal gap G1 formed of the connector housing and a cover, a second seal gap G2 formed of the connector housing and the base and a third seal gap G3 formed of the base and the cover are included; the first seal gap G1 is formed of a terrace slope portion gap G1b and an outer step flat portion gap G1a and an inner step flat portion gap G1c that are in communication with the terrace slope portion gap G1b; a gap setting protrusion for limiting the gap width is provided at least in the first seal gap G1; and, between the connector housing and the cover, a horizontal movement limitation member are provided for limiting the relative positional relationship between the connector housing and the cover.