The present invention is to present a sample analyzer for analyzing a target substance in a sample by carrying out a target substance separating process for separating a complex containing the target substance and a magnetic particle from other substances other than the complex. The sample analyzer executes the target substance separating process with respect to a second container held by a second holder with a second nozzle while executing the target substance separating process with respect to a first container held by a first holder with a first nozzle, and completes the target substance separating process with respect to the first container with the first nozzle and completes the target substance separating process with respect to the second container with the second nozzle.