Malik was born in Pematang Siantar,North Sumatra, Dutch East Indies to Abdul Malik Batubara and Salamah Lubis. He is from a Batak Mandailing Muslim family of Batubara clan.After completing Junior High School, he received his first job as a shopkeeper, filling in time by reading books and increasing his knowledge.
Malik quickly developed an interest in politics and aged just 17, became the Chairman of the Pematang Siantar branch of Partindo (Indonesia Party). In this position, Malik campaigned for the Dutch Colonial Government to grant independence to Indonesia. As a result of this, Malik was put in prison for disobeying the Colonial Government's ban on political assemblies. Once he was freed, Malik left Pematang Siantar for Jakarta.