Thomas played college basketball for the San Diego State (SDSU) Aztecs, where he twice earned All-Mountain West Conference (MWC) second-team honors. Before signing with the Bulls, he played professionally for the San Antonio Spurs and Golden State Warriors in the NBA, the Los Angeles D-Fenders, Austin Toros, and Rio Grande Valley Vipers in the NBA Development League, Mobis Phoebus in the Korean Basketball League, and Maccabi Tel Aviv in Israel.
Thomas was born in Columbia, Missouri, to his father, also named Malcolm Thomas, and Lori Dawson. His father was an honorable mention All-American basketball player at Missouri and drafted in the sixth round of the 1985 NBA Draft by the Los Angeles Clippers.
The younger Thomas was raised by his mother and aunts, while his father was not always around. Thomas played at Crawford High School in San Diego, California, helping Crawford to a California Interscholastic Federation (CIF) section title in his senior year.
Thomas averaged 12.5 points and 8.8 rebounds as freshman at Pepperdine University. He transferred to San Diego City College and averaged 21.1 points, 12.9 rebounds and 3.9 blocks and was named California Community College Athletic Association (CCCAA) co-Most Valuable Player (MVP) and the Pacific Coast Conference Player of the Year. He declared early for the 2009 NBA Draft, but withdrew after one NBA workout.
He went on to play two seasons at SDSU and twice earned All-MWC second team honors. In his senior year, he was named 2011 All-MWC defensive team after finishing second in the conference in rebounding and blocked shots. The team advanced to the NCAA Sweet 16 that season. He ended his two-year career with the Aztecs as the school’s second leading all-time shot blocker and ranked eighth all-time in both rebound average and field goal percentage.
Thomas went undrafted in the 2011 NBA Draft. During the NBA lockout that summer, he signed a $350,000 contract to play a season for Mobis Phoebus in the Korean Basketball League. Most overseas rookies made about $100,000–$150,000. The team released him in November 2011, despite his averaging 21 points, 11 rebounds, three blocks, and three assists. They wanted a more veteran player, but agreed to pay the remainder of Thomas' salary.
Thomas was signed by the Los Angeles Lakers on December 13, 2011. On December 17, he was assigned to the Los Angeles D-Fenders by the Lakers, and was recalled the next day. He was waived by the Lakers before the start of the 2011–12 season. He was signed by the D-Fenders on December 28.
On January 11, 2012, Thomas was then signed by the San Antonio Spurs, where he was reunited with former Aztec teammate Kawhi Leonard. He played in his first NBA game on January 13 against the Portland Trail Blazers, getting one rebound in two minutes of garbage time. Thomas was assigned to the Austin Toros on January 30. On February 7, the Spurs waived Thomas. He joined the D-Fenders again on February 9.
Later that season, he signed with the Houston Rockets, who assigned him to the Rio Grande Valley Vipers. He then rejoined the D-Fenders, with whom he played in the D-League finals.
On October 3, 2012, Thomas signed a one-year contract with Euroleague giant Maccabi Tel Aviv of Israel. In competition in Israel, he averaged 7.4 points, 5.3 rebounds, and 1.3 blocks, and in Euroleague competition he had a double-double of 14 points and 11 rebounds in 26 minutes in a 70–68 victory over Italian Montepaschi Siena in mid-October. However, after Tel Aviv signed 6-foot-11 Croatian Darko Planinić, his minutes decreased. Thomas was waived by Maccabi Tel Aviv in February 2013.
On March 5, he rejoined the Los Angeles D-Fenders. On March 8, Thomas was called up from the D-League and signed a 10-day contract with the Golden State Warriors. He was assigned to the Santa Cruz Warriors of the NBA D-League on March 12, 2013. He was recalled a day later.
On March 19, 2013, Thomas signed a 10-day contract with the Chicago Bulls. He signed a second 10-day contract on March 29, 2013, and signed for the remainder of the season on April 8, 2013.
Thomas has a daughter, Mikeala, who was born in 2009.