A controller for a machine tool has a program storage section in which an NC program is stored, a program analyzing section analyzing the NC program block by block in sequence and extracts operation commands for a feed mechanism, an execution control section executing the extracted operation commands and thereby controlling the feed mechanism, e program editing section changing the NC program, and a change information storage section in which change information relating to the changed portion of the NC program is stored. The execution control section, when executing the operation commands, checks whether the block of each operation command is the block immediately preceding a block relating to the changed portion, and when judging that it is the immediately preceding block, temporarily stops the operation of the feed mechanism before or after the execution of the operation command.