A waterproof housing structure for portable optical analyzer mainly comprises a hard upper casing, a lower casing and a fastening element. The hard upper casing contains an outer rim and an inner rim. The lower casing contains a hard inner shell and a pliable cap. The hard inner shell has a trapezoidal rim which has a first trapezoidal surface and a second trapezoidal surface lower than the first trapezoidal surface. The pliable cap wraps a portion of outer surface of the hard inner shell, and has an outer edge and an inner edge mating the upper casing. The fastening element fastens the hard upper casing to the lower casing. Thus the two irregular rims and edges can be coupled to prevent liquid permeation. Fabrication and assembly during production or repair and maintenance are simpler. It also improves grasp feeling and anti-slipping effect on the handgrip of the portable optical analyzer.