Mysterious Pirate Jewels 3 is a timed, connect-style, match-3 game that features a grid of hexagon shapes. Across 45 levels, the player connects and releases jewels, also known as hexes, from the grid in groups to break and remove colored backgrounds. Their primary goals are to earn standard and bonus points through matches before time runs out and complete all the levels.
Instead of using a limited number of connecting lines, the player connects three or more matching jewels with color-matched arrows in any direction. When the player completes a match, the game makes the matching hexes disappear in sparkles and then fills in the empty spaces on the grid with new hexes. It immediately removes any pink background color from the grid. With any other color, such as blue, it removes only the top color. The player must perform another match to remove the pink.
Mysterious Pirate Jewels 3 charges several boosters in the lower-right corner after the completion of each match. The player can use a back arrow to undo their last move. Over time, the same button transforms into two arrows that shuffle the tiles. They can also drag a hammer to the grid to release matching and non-matching jewels.
During play, the game also fills spaces with special items, including rainbow-colored oval hexes that act like jokers to match any jewel, a glowing light-colored oval ball that acts like lightning to remove all hexes that match its color, and an hourglass that adds more time to the clock.