The invention relates to the technical field of protein detection, and particularly relates to a method and system for detecting a protein expression quantity and a protein aggregate quantity of a cell culture. The detection method comprises the following step of: carrying out gradient elution and detection on the cell culture by an affinity chromatographic column and a size exclusion chromatographic column which are connected in series, wherein mobile phases for gradient elution comprise: a mobile phase A which comprises 10 to 200mM monosodium phosphate and sodium hydrogen phosphate mixture and 50 to 500mM sodium chloride and has pH of 6.8 plus and minus 0.5; and a mobile phone B which comprises 10 to 200mM glycine and 20 to 300mM sodium chloride and has pH of 2.5 plus and minus 0.5. According to the detection method disclosed by the invention, the affinity chromatographic column and the size exclusion chromatographic column are connected in series; a certain mobile phases are adoptedto carry out gradient elution; the protein expression quantity and aggregate percentage in the cell culture can be simultaneously detected; and the method and the system are simple, convenient, easyto operate, low in cost and reliable in result.