How do I make command blocks work up to 1000000 blocks away

I am trying to make this survival map but it will be using many command blocks. I don't want this big cube of bedrock so I want my command blocks to be 1000000+ blocks away, but the command blocks do not run. How do I make it work that far away? I am in Minecraft 1.12 or up when the next update comes out.

Have you considered using functions (and particularly using gamerule gameLoopFunction <function file>) instead? You can replace most of your command blocks fairly easily, although you'll probably still want some to conditionally call some other functions (either after a testing command (like testfor or testforblock, among others) or execute-ing against a selector (and using the new @s selector in the function)). Conditional operation within functions is in some cases easier to do, and in others a bit harder, but for the most part is still pretty easy.

If you can run everything off a single gameLoopFunction (that possibly calls other functions), then you don't have to worry about a single command block in your world. If you do need some command blocks, for whatever reason, then just make sure to place them in the world spawn chunks. You did make sure to set the world spawn to (0,0) when you started, right? That's the first step in the map-maker's handbook. A small bedrock lined room at the bottom of the world isn't going to be much of a hindrance, especially if it's only 5 blocks tall and contains only a few dozen command blocks. Most of the time, it's pretty easy to hide something like that.