An object of the present invention is to make short a manufacturing time at a time of switching a kind of a filling drink. In a cleaning method of a drink filling system provided with a drink supply pipe line for supplying a drink to a filling machine (2) and an aseptic chamber (3) surrounding at least the filling machine, the cleaning method is performed by executing program including at least two of first, second and third programs, wherein the first program corresponds to an aseptic carbonated drink and executes a COP treatment performed for an interior of the aseptic chamber and a CIP treatment performed for an interior of the drink supply pipe line, the second program corresponds to a high acidic drink and executes the COP treatment and an SOP treatment performed for the interior of the aseptic chamber and a CIP treatment and an SIP treatment performed in the interior of the drink supply pipe line, and the third program corresponds to a low acidic drink and executes the COP treatment and the SOP treatment performed for the interior of the aseptic chamber and the CIP treatment and the SIP treatment performed in the interior of the drink supply pipe line, and wherein either one of the three programs is enabled to be selectively executed, and in a case where the drink is an aseptic carbonated drink, the first program is selected, in a case where the drink is a high acidic drink, the second program is selected, and in a case where the drink is a low acidic drink, the third program is selected, to thereby clean the interiors of the aseptic chamber and the drink supply pipe line before filling of the drink in accordance with the selected program.