An apparatus and method for analyzing malware in a data analysis system are provided. The apparatus includes a data analysis unit and a controller. The data analysis unit sorts data into primary harmful data and primary harmless data using screening data information of malicious code information and virus information. The controller screens or deletes the primary harmful data, and sends a request for precision analysis of the primary harmless data to a server. The data analysis unit sorts secondary harmful data from the primary harmless data using the precision analysis result received from the server.