| Lane/Order | BIB | ATHLETE | Seeding Time | Note | |
|---|---|---|---|---|---|
| 1 | 232 | KOTA MARUDU | VILLEY VICKY KAINON | 47.11 | q |
| 2 | 799 | TENOM | AZZALI PILIMON | 44.90 | q |
| 3 | 549 | PUTATAN | DOMINIC YONG FOOK PAU | 49.54 | Q |
| 4 | 717 | TAMBUNAN | JACKLEE VELLERY JANURIS | 49.65 | Q |
| 5 | 865 | TUARAN | BRAELDYENN WONG ZHENG JIA | 45.39 | q |
| 6 | 122 | KINABATANGAN | MOHAMMAD HAIQAL BIN JAMAL | 54.21 | Q |
| 7 | 786 | TELUPID | ABENJO ANDURUS | 42.25 | q |
| 8 | 816 | TENOM | EDDY EDLEY YUWANG | 53.16 | Q |
| 9 | 662 | SEMPORNA | MOHAMMAD FAZRIN AZRI BIN ABDUL SYAMRI | 49.65 | Q |
| 10 | 231 | KOTA MARUDU | FREDDY HEE RONG CHUEN | 43.20 | q |
| 11 | 584 | RANAU | ERICKSON JAKSON | 51.13 | Q |
| 12 | 710 | TAMBUNAN | FEBIANS VITUS | 52.58 | Q |