| # | Title | Length |
|---|
| 1 | The Military System -X- (Operation Explanation, Ranking) | 0:56 |
| 2 | Barracks -X- (Character Select) | 0:41 |
| 3 | Judgment -X- (Stage 1-1) | 2:01 |
| 4 | Steel Beast 6Beats -X- (Boss Theme A) | 2:02 |
| 5 | Prehistoric Site -X- (Stage 2-1) | 2:01 |
| 6 | The Cenotaph -X- (Stage 2-3) | 2:01 |
| 7 | First Contact -X- (Boss Theme B, Stage 6-2) | 2:02 |
| 8 | Livin On The Deck -X- (Stage 3-1) | 2:01 |
| 9 | Assault Theme -X- (Boss Theme C, Stage 6-1) | 2:03 |
| 10 | Back To The China -X- (Stage 4-1) | 2:12 |
| 11 | New Godokin Street -X- (Stage 5-1) | 2:02 |
| 12 | Kiss In The Dark -X- (Stage 5-2) | 2:01 |
| 13 | Metamorphosis -X- (Stage 5-3) | 2:01 |
| 14 | Gravestone -X- (Game Over) | 0:10 |
| 15 | Final Attack -X- (Stage 6-3) | 2:02 |
| 16 | End Title Again -X- (Final Performance) | 0:24 |
| 17 | MS_X Ending -X- (End Credits) | 2:45 |
| 18 | Carry Out -X- (Stage Clear) | 0:09 |
| 19 | The Military System (Operation Explanation, Ranking) | 0:53 |
| 20 | Barracks (Character Select) | 0:41 |
| 21 | Blue Water Fangs -The Island of Dr. Moreau- (Main Theme From METAL SLUG 3) (Stage 1) | 2:10 |
| 22 | Marine Diver (Stage 1 Altanative Route~Deep Sea) | 1:45 |
| 23 | The Unknown World (Stage 1 Altanative Route~Core Facility, UFO Interior Passage 1) | 2:20 |
| 24 | Steel Beast 7Beats (Boss Theme A) | 2:15 |
| 25 | Midnight Wandering (Stage 2) | 2:19 |
| 26 | Devil's Snow Cave (Stage 1 Altanative Route~Cave of Ice) | 1:51 |
| 27 | Metamorphosis (Boss Theme B) | 1:52 |
| 28 | The Shallow Sea (Stage 3) | 1:41 |
| 29 | Hard Water (Stage 3 Altanative Route~Underground Channel) | 2:38 |
| 30 | Assault Theme (Stage 3 Altanative Route~Bridge, Stage 5-2) | 2:31 |
| 31 | Secret Factory (Stage 3 Altanative Route~Armory) | 2:10 |
| 32 | Desert (Stage 4) | 1:49 |
| 33 | Pyramid (Stage 1 Altanative Route~Pyramid) | 1:31 |
| 34 | The Cenotaph (Stage 4 Altanative Route~Ancient Ruins) | 2:02 |
| 35 | The Japanese Army (Stage 4 Altanative Route~Ex-military Hideout) | 1:55 |
| 36 | Into the Sky (Stage 5-1) | 2:10 |
| 37 | The Kidnapping (Alien Appearance) | 0:34 |
| 38 | Into the Cosmos (The Void of Space) | 2:30 |
| 39 | Kiss In The Dark (Enemy UFO Interior) | 1:35 |
| 40 | First Contact (UFO Interior Passage 2) | 1:56 |
| 41 | Bioinformatics (UFO Interior Passage 3) | 2:10 |
| 42 | Escape (UFO Escape) | 1:59 |
| 43 | Final Attack (Final Boss) | 2:15 |
| 44 | End Title (Final Production~Staff Roll) | 2:28 |
| 45 | Gravestone (Game Over) | 0:09 |
| 46 | Carry Out (Stage Clear) | 0:08 |
