A series of adjustable padded support clamps attach to pontoon boat rectangular rails to support the structural frame members of a boat cover. Each two-part support clamp comprises a first padded square C-shaped channel bracket member having an aperture in a top arm thereof, and a second post and plate member. The post protrudes up through the aperture in the top arm of the C-shaped channel bracket to receive a coupling of a frame member of the boat cover. A bottom padded plate of the second member is adjustably secured against a top of the boat rail by turning one or more adjusting screws to draw the padded bottom arm up securely against a bottom of the boat rail.