The invention discloses a protein rapid detection method based on a matched microalgae protein characteristics sequence label and a system thereof; the method includes steps of collecting a microalgae sample, and acquiring its protein sequence set, converting it to a standard protein sequence set, performing splitting and configuration treatment, and converting the protein sequence set to a key/value pair list specific to a given sequence segment; after summarizing the key/value pair list, performing an intersection operation; when the result is not empty, confirming that one data of the data set contains the characteristic protein sequence. The system mainly includes a detection data input module, a key/value pair list module, a detection identification module, a characteristic value intersection operation module, and an output module. Through indexing the protein sequence, the method and the system judge the protein homology and similarity level; by comparing with the traditional method of comparing data one by one, the algorithmic identification accuracy is and efficiency are significantly improved, the indexing efficiency is greatly promoted; the method and system have good practicability, and the algorithmic time complexity is low, the performance is high; therefore, the method and the system are significant to study proteomics.