| 1 | Mohammad Ibnu Sabilillah | 1:01.98 | 1:08.77 | 1:08.16 1:05.65 1:01.98 1:12.50 1:37.74 |
| 2 | Vincent Hartanto Utomo | 1:02.46 | 1:12.08 | 1:18.06 1:02.46 1:29.62 1:08.38 1:09.79 |
| 3 | Andre Febriato Jonathan | 1:14.88 | 1:26.01 | 1:30.80 1:22.54 1:37.84 1:24.70 1:14.88 |
| 4 | Achmad Rizki Zakaria | 1:28.56 | 1:37.32 | 1:30.87 1:43.26 1:37.84 1:58.26 1:28.56 |
| 5 | Stephen Adhisaputra | 1:33.89 | 1:49.34 | 1:49.32 1:33.89 1:53.88 2:08.54 1:44.82 |
| 6 | Jundi Ahmad Alwan | 1:48.92 | 1:58.13 | 2:25.94 1:48.92 1:53.74 1:56.92 2:03.74 |
| 7 | Ahmad Fauzi Wibowo | 1:35.35 | 2:04.97 | 2:10.60 1:57.68 1:35.35 2:06.62 2:22.59 |
| 8 | Tanto Prabowo | 2:04.87 | 2:11.02 | 2:13.59 2:04.87 2:09.35 2:10.12 2:24.37 |
| 9 | Hafizh Dary Faridhan Hudoyo | 2:35.04 | 2:48.14 | 2:43.45 2:35.04 2:56.60 3:29.64 2:44.38 |
| 10 | Cendy Cahyo Rahmat | 2:33.96 | 2:59.04 | 2:46.36 2:33.96 3:05.37 3:30.41 3:05.38 |
| 11 | Wilson Alvis (陈智胜) | 2:30.96 | 2:59.54 | 2:58.50 3:05.45 2:54.67 2:30.96 3:09.52 |
| 12 | Ahsanul Wildan | 2:51.55 | 3:07.37 | 3:14.91 2:51.55 3:37.41 3:13.52 2:53.69 |
| 13 | Fredi Dwi Harminto | 4:32.77 | — | 4:32.77 5:22.65 — — — |
| 14 | Kalim Fazalurrohman | 4:38.03 | — | 6:45.84 4:38.03 — — — |
| 15 | Andi Alvin Adhyaksa Putra | 5:49.55 | — | 7:13.01 5:49.55 — — — |
| 16 | Kevin Timothy | 5:51.85 | — | 5:51.85 DNS — — — |