The invention discloses a method and a system for transmitting upstream signals of a passive optical access network user, belongs to the technical field of fiber optical communication, and solves the problem about upstream signal conflicting of the user so as to improve transmission rate. The method includes: respectively modulating user information on N orthogonal waveform generators, converting into composite output optical signals via a laser; converting the received composite output optical signals into composite electrical signals, and separating N paths of same sub composite electrical signals to recover N paths of different user information. In the system, a signal transmitting terminal comprises N different orthogonal waveform generating circuits, an electric combiner and the laser, a signal receiving terminal comprises a photoelectric detector, an electric branching unit, N relative circuits, N judging regenerative circuits and the N orthogonal waveform generators. Requirements for frequency offset and phase noise are low, dependence on electronic chips is reduced, access capability of user-side data is greatly improved, and the structure and the protocol of a passive optical access network are simplified.