You would use something like "System every 1 second" to add a value to a time variable (ie. timeVar). You would then need a Text object or GUI text to display the timeVar for player. Then when its time to calculate bonus you would do whatever math you wanted via events from other variables like collected coins, bonus objects, etc..
Ie. timeVar-levelTime (variable value for max time one would do level in base value so the lower timeVar is the more "bonus" they get) x [coinVar+bonusObjectVar] = scoreVar (to display)...
Its a complex system between variables to store info and UI to display it. You will need to piece it together in a way that feels right for your game.