Your Win Condition
Survive until six. Kill him at first item.
General Strategy
3Q>E Max Farm with q and e until six. Dodge side to side to avoid getting hit by his e. Go Dorans Shield. You can usually get away with running a more greedier rune set-up like conditioning or sorcery.
Trading Patterns
Trades against Malphite are almost never positive against him. Try to avoid fighting him. His attack speed slow means you are going to do zero damage against him despite the fact you do ap damage into his armor. You can only really do decent damage against him at level 16 and at that point you are already teamfighting.
Wave Management
You want the wave near your turret always in this matchup so he cannot q spam you or ult onto you. Try not to push the wave when you are farming or poking with q.
Their Win Condition
Mordekaiser wants to poke you with qs and look for very heavy trades if he ever lands his e onto you. Once his pull goes off, he can easy activate his passive and utilize the movement speed he gets from it to run you down.