The invention discloses a file processing method and device for a distributed system. One specific execution mode of the method comprises the steps that a file containing predetermined identifiers is received; the file is divided into multiple subfiles according to the size of the file, the quantity of the predetermined identifiers in the file and the quantity of servers contained in the distributed system, wherein all the subfiles contain the same quantity of predetermined identifiers; responding to file processing requests sent by at least one of the servers contained in the distributed system, the subfiles are sent to the corresponding servers for parallel processing of the file. By the adoption of the execution mode, the processing efficiency of gene information files is improved, and load balancing is achieved.