Cooked custard pies are notorious for cracking. This issue can stem from several different sources, including mixing technique, baking temperature, and the cooling process.
When mixing a cooked custard filling, take extra care not to beat air into it. Too much air in the filling will cause it to inflate in the oven and then collapse, which causes cracking. This means it is also extra important that all of your ingredients are truly at room temperature before mixing, so that they will easily blend together to make smooth filling.