The invention provides application of a configurable batch report in a lyophilizer. The main technical means is as follows: using reporting software of the configurable batch report on PC in a control system of the lyophilizer, using an SQL database to store the data and accessing IntellutioniFIX historical data and real time data, Excel and PDF printer applications via the COM interface. Through application of the configurable batch report in the lyophilizer, the contents and the format of the report can be flexibly set to adapt to the variation of the process, the PDF report can be established and the process formula, process data, fault alarm, periodic events, operating records, etc can be reported. The configurable batch report can be used in all the periods of the lyophilizer and a plurality of report templates can be configured in the same period, thus facilitating evaluation of the effectiveness of the production process.