True Love Story 3 places the player in the shoes of a young male protagonist experiencing his third year of Junior High with the goal of confessing his love to one of a number of female peers. As the year opens he is introduced to the girl he has long had a crush on, Aotsuki Takane, by his twin sister who commutes to the same school, Kaname.

Consistent with other games in the series, True Love Story 3 features an unusually high amount of player interactivity in proportion to story content. Brief, stock dialogs are often repeated when the player character encounters characters he has already met several times.

The game tracks characters' "level of friendship" (友人度) and "level of affection" (恋愛度) towards the player character on a triangular diagram that the player can learn the status of regularly by consulting with his twin sister at the end of a day. Instead of playing each day of the school year, the player selects "try-your-best days" (頑張る日), the frequency of which affects his level of enthusiasm (やる気), which in turn influences the occurrence of special events.

But the most distinguishing feature of the game and of the series as a whole is its unique conversation system. At the end of a weekday, if the weather is sunny, the player has three chances to try to meet a girl who he can invite to walk home with (or be invited to walk home with) and the invite, if successful, leads to a complex conversation mode in which numerous topics can be selected, the goal being to raise the girl's "hearthrob gauge" (ときめきゲージ) without filling up her "pounding heart" （ドキドキハート） and possibly invite her out on a date before the walk home concludes.