Mamat thrived in the perfect morning condition of the course with six birdies for a five-under-par 66.
He closed the last four holes with three birdies for a two-day score of seven under 135.
Two shots behind is Arie Irawan, who carded five-under-par 66 in Thursday's round.
In a chat with media, Mardan said he had to stay patient on the tough course, "It was important to stay patient out there because I could not build on my advantage early on but fortunately, I got into a stride towards the end of the round and drained back-to-back birdies from the sixth.
"Overall, it was a good round but I need to keep my putting rhythm going if I'm going to have a chance of winning this tournament," he added.
Japan's Masaru Takahashi shared third place alongside Jay Bayron of the Philippines with three-under 139.
Leading second round scores:
135 – Mardan Mamat (SIN) 69-66
137 – Arie Irawan (MAS) 71-66
139 – Masaru Takahashi (JPN) 73-66, Jay Bayron (PHI) 72-67
140 – Pipatpong Naewsuk (THA) 69-71
141 – Sukree Othman (MAS) 73-68, Koh Dengshan (SIN) 75-66, Shaaban Hussin (MAS) 70-71
142 – Ratchapol Jantavara (THA) 70-72, Sutijet Kooratanapisan (THA) 69-73, Solomon Emilio Rosidin (MAS) 70-72
143 – Joeh Seik (INA) 72-71, Lim Eng Seng (MAS) 72-71, Nicholas Pua (MAS) 73-70, Natthapong Niyomchon (THA) 74-69, Song Gyu Yoo (KOR) 72-71, Wisut Artjanawat (THA) 70-73, Airil Rizman Zahari (MAS) 69-74, Kwanchai Tannin (THA) 72-71, Ben Leong (MAS) 74-69.