The invention discloses a processing structure of a coastal soft foundation, comprising longitudinal troughs, transverse troughs and vertical shafts. The longitudinal troughs are distributed on two outer sides of the highway subgrade fill, and an impermeable geomembrane is arranged on one side, far away from the highway subgrade fill, of the longitudinal troughs; the longitudinal troughs have a certain longitudinal slope, the depth is bigger than that of the soft foundation layer, and an embankment layer, the soft foundation layer and a bearing stratum form the highway subgrade fill from top to bottom in sequence. The transverse troughs are distributed on the coastal highways and intersected with the longitudinal troughs; the transverse troughs have a certain slope, the depth is bigger than that of the soft foundation layer, and slope pits are formed in the intersection positions of the transverse troughs and the longitudinal troughs. The vertical shafts are formed in the intersection positions of the transverse troughs and the longitudinal troughs. In the construction process, the transverse troughs and the longitudinal troughs are filled with rubble or gravel. The processing structure of the coastal soft foundation has an obvious effect for the coastal marine deposit soft foundations, is small in the work amount and avoids lateral movement of the soft foundations.