The new base of operations is Yukumo Village. This village has a feudal Japanese feel to it, both from its design to its residents. Now the Felynes train in the farm and have more training options like the marathon training in which the Felyne runs around the farm. The player can take two Felynes out with them on a single player quest, up from the single companion of Monster Hunter Freedom Unite. When you take Felynes out on quests, monster attacks are divided between the player and the companions, making hunts easier. Also new to Monster Hunter Portable 3rd is the ability to customize the Felyne companions' equipment. Doing so will change the creature's physical appearance and properties. The player will be able to customize the Felynes in three areas: weapon, head parts and torso parts. A new field introduced in the game is Misty Peaks (渓流, Keiryū). All the hunting fields in Monster Hunter Tri, along with the addition of the Misty Peaks field are included in Monster Hunter Portable 3rd. Underwater quests, however, have been completely removed, therefore maps such as the Deserted Island and Flooded Forest have been revised to work around this. Not all monsters from Monster Hunter Tri are present in Monster Hunter Portable 3rd – Lagiacrus, Gobul, and Ceadeus have been removed. Zinogre, the flagship monster of the game is shown on the cover art.
The Guild Hall now features a hot spring, similar to the Felyne Kitchen from previous games, which can be upgraded by clearing special 'Hot Spring Quests' which upgrade the effects of the hot spring, as well as the Felyne Whim Skills, which can now be chosen and selected by the player.
All weapon classes from previous games (Great Sword, Long Sword, Sword and Shield, Dual Blades, Hammer, Hunting Horn, Lance, Gunlance, Switch Axe, Light Bowgun, Heavy Bowgun and Bow) are present in the game. The four classes which were not present in Tri (Dual blades, Hunting Horn, Gunlance and Bow) have been revised. The equipment creation and fortification systems received a variety of changes. Producer Ryozo Tsujimoto claimed that this area of the game will keep what was good from Monster Hunter Freedom Unite and Monster Hunter Tri and add new elements.