With the Mets, Matsui hit home runs in his first plate appearance in each of the 2004, 2005, and 2006 seasons. According to the Elias Sports Bureau, he is the only Major League player to hit a home run in his first plate appearance of his first three seasons. The only other player to hit a home run in even his first at-bat of three consecutive seasons was Ken Griffey, Jr. In 2004, Matsui homered on the first pitch from Russ Ortiz of the Atlanta Braves leading off the first inning, in 2005, on the sixth pitch from Paul Wilson of the Cincinnati Reds with one out in the first inning, and in 2006, on the fourth pitch from Jake Peavy of the San Diego Padres with no outs in the top of the third. The third home run is notable for being an inside-the-park home run. He slid into home as his former Met teammate Mike Piazza was blocking the plate.
Matsui played 114 games in 2004 (the most games he has played so far in his MLB career). He hit .272 with 125 hits, 32 doubles, 2 triples, 7 home runs, 44 RBI, 65 runs, 14 stolen bases, 5 sacrifice hits, 40 walks and 182 total bases. His hits, doubles, home runs, RBI, walks, and total bases currently remain career highs.
Based on his performance in Japan, Matsui was expected to excel defensively as a shortstop with the Mets. However, in 2004, Matsui committed many errors and misjudgments at the position, and was made the second baseman for 2005. He was also plagued by injuries, which were not a problem for him in Japan. His offensive production was also much lower than anticipated. By mid-2005, he was no longer an everyday player, sharing time at second base with Miguel Cairo and Marlon Anderson. Matsui finished the season batting .255 with three home runs and 24 RBI.