| Lane/Order | BIB | ATHLETE | Seeding Time | Note | |
|---|---|---|---|---|---|
| 1 | 513 | PHILIPPINES | JOHN CLINTON MITCHEL ABETONG | 50.62 | q |
| 2 | 423 | THAILAND | AMOS MAHAKANJANA UNGER | 50.08 | q |
| 3 | 104 | MALAYSIA | MUHAMAD QARLIFF KUYT BIN ABDULLAH | 49.84 | Q |
| 4 | 511 | PHILIPPINES | KIAN LABAR | 48.23 | Q |
| 5 | 309 | SINGAPORE | SEAN RUSSELL TAY | 50.24 | Q |
| 6 | 214 | INDONESIA | RANGGA ADE | 49.69 | Q |
| 7 | 422 | THAILAND | ADISAK PORNSOMPHOT | 49.16 | Q |
| 8 | 113 | MALAYSIA | KABEENESH AL MANICKAM | 50.33 | Q |