- New York Mets traded Tom Parsons to the Houston Astros for Jerry Grote on October 19, 1965.
- New York Mets traded Gary Kroll to the Houston Astros for John Weekly on January 6, 1966.
- New York Mets purchased Ron Taylor from the Houston Astros on February 10, 1967.
- New York Mets traded Derrell Griffith to the Houston Astros for Sandy Alomar on March 24, 1967.
- New York Mets selected Jack DiLauro in free agent draft on December 1, 1969.
- New York Mets traded Tommie Agee to the Houston Astros for Rich Chiles and Buddy Harris on November 27, 1972.
- New York Mets traded Ken Boswell to the Houston Astros for Bob Gallagher on October 29, 1974.
- New York Mets traded Stan Hough and Randy Rogers to the Houston Astros for Bruce Bochy on February 11, 1981.
- New York Mets traded John Csefalvay to the Houston Astros for Gary Rajsich on April 3, 1981.
- New York Mets traded Mike Scott to the Houston Astros for Danny Heep on December 10, 1982.
- New York Mets traded Gerald Young, Mitch Cook and Manny Lee to the Houston Astros for Ray Knight on August 28, 1984.
- New York Mets traded Steve LaRose and Nicky Davis to the Houston Astros for Dan Schatzeder on September 10, 1990.
- Houston Astros signed Kevin Bass of the New York Mets as a free agent on January 7, 1993.
- New York Mets traded Juan Castillo and Todd Beckerman to the Houston Astros for Pete Harnisch on November 28, 1994.
- Houston Astros signed Bill Spiers of the New York Mets as a free agent on January 10, 1996.
- New York Mets traded Tim Bogar to the Houston Astros for Luis Lopez on March 31, 1997.
- New York Mets signed free agent Todd Haney of the Houston Astros on December 6, 1997.
- New York Mets traded Carl Everett to the Houston Astros for John Hudek on December 22, 1997.
- New York Mets traded Roger Cedeno, Octavio Dotel and Kyle Kessel to the Houston Astros for Derek Bell and Mike Hampton on December 23, 1999.
- Houston Astros signed Jim Mann of the New York Mets as a free agent on January 3, 2001.
- Houston Astros signed C.J. Nitkowski of the New York Mets as a free agent on December 21, 2001.
- New York Mets signed free agent Pedro Astacio of the Houston Astros on January 16, 2002.
- New York Mets traded David Weathers and Jeremy Griffiths to the Houston Astros for Richard Hidalgo on June 17, 2004.
- New York Mets traded Dan Wheeler to the Houston Astros for Adam Seuss on August 27, 2004.
- New York Mets signed free agent Carlos Beltran of the Houston Astros on January 11, 2005.
- Houston Astros signed John Franco of the New York Mets as a free agent on January 23, 2005.
- Houston Astros signed David Newhan of the New York Mets as a free agent on January 28, 2008.
- New York Mets claimed Fernando Nieve on waivers from the Houston Astros on March 14, 2009.
- Houston Astros signed Jon Switzer of the New York Mets as a free agent on December 11, 2009.
- Houston Astros signed Cory Sullivan of the New York Mets as a free agent on January 20, 2010.
- New York Mets signed free agent Tim Byrdak of the Houston Astros on January 21, 2011.
- Houston Astros claimed Fernando Martinez of the New York Mets on waivers on January 11, 2012.
- Houston Astros signed Kyle Farnsworth of the New York Mets as a free agent on May 17, 2014.
- New York Mets traded Scott Manea, Luis Santana and Ross Adolph to the Houston Astros for J.D. Davis and Cody Bohanek on January 6, 2019.
- New York Mets traded Blake Taylor and Kenedy Corona to the Houston Astros for Jake Marisnick on December 5, 2019.
- New York Mets traded Justin Verlander to the Houston Astros for Ryan Clifford and Drew Gilbert on August 1, 2023.
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