His pairing opposite actress Kushboo and Meena became popular in this decade. The box office hits of the pair Kushboo-Sathyaraj include Nadigan, Bramma, Rickshaw Mama, Kalyana Galatta, Suyamvaram, Malabar Police and Unnai Kann Theduthey, whereas Thozhar Pandian and Veeranadai were not successful at the box office. The on-screen pair of Sathyaraj-Meena together had average grossers such as Thai Maaman, Maaman Magal, Vallal and later in 2003 with Aalukkoru Aasai. His chemistry with actors Goundamani and Senthil has been well received and appreciated by the public and hence they have appeared in many movies together from Vaazhkai Chakkaram in 1990.
Sathyaraj re-invented himself as a romantic hero with the 2002 film Vivaramana Aalu, as a hero Maaran and with his performance in the comedy film Aalukkoru Aasai in 2003. Sathyaraj and director Sakthi Chidambaram's combination gave 3 consecutive films, Ennamma Kannu, Maha Nadigan and Englishkaran. Ennama Kannu was a super hit. Few films like Ramachandra, Sena, Azhagesan, and Gowravargal received negative reviews in this decade. He co-starred with his son Sibiraj for the first time in Jore which was average. Bizhat described "It's interesting to watch the father – son combination together in Jore. Sathyaraj then acted with his son in 3 more films Mannin Maindhan, Vetrivel Sakthivel and Kovai Brothers, in which the two were seen as brothers. In 2007, he produced a Tamil film Lee, starring his son .