The invention provides a method and device for adaptively decoding a serial communication protocol of a merging unit. An optical signal is converted into a level signal; according to the change time of the level signal in a statistical period, type judgement on a setting optical signal and protocol matching on a data optical signal are carried out; and analysis decoding on the setting optical signal and the data optical signal is separately carried out according to the type of the setting optical signal and protocol matching on the data optical signal. According to the method and the device provided in the invention, the type and the polarity of the setting optical signal do not need to be obtained in advance; pre-configuration of software is unnecessary; two setting optical signals and three data optical signals can be adaptive; the adaptation is high; functional unification and hardware design unification of the merging unit are realized; repetitive design and verification costs of the merging unit are reduced; and simultaneously, the material cost and the human cost are also reduced for various links of the merging unit, such as producing, debugging, operating and maintaining.