Многие пути ведут в Рим:
1 способ:
LOAD DATA LOCAL INFILE 'file.txt'
INTO TABLE t1 (column1, column2, column3);
другой способ:
CREATE TABLE `import` (
`column1` int(11) NOT NULL,
`column2` varchar(128) NOT NULL,
`column3` varchar(128) NOT NULL
) ENGINE=MyISAM CHARSET=utf8;
LOAD DATA LOCAL INFILE 'file.txt'
INTO TABLE import
(column1, column2, column3);
INSERT INTO destination_table (columnA,columnB,columnC)
SELECT column3, column1, column2 FROM import;