A friend asked me to hook up his water pump. He has the red black yellow and green wires running to the house, which he wants hooked up to the box. This is not right is it. I thought that power came from main box to a control box and these wires hooked to control box from pump?

If the "main box" is the "House Load center" or what people call the "Fuse box", the "Fuse box" should not be used for splicing.

Load center to controls.
Control to pump.

Well keep it simple I don't think you understand. The control box I was referring to is the pump control box that is fed from the main circuit breaker pannel. The control box usually has a pressure switch for the pump and you can disconect the pump with the control box. I just want to know how to wire control box to pump.

This sounds dangerous. You state that the control box usually has a pressure switch - that is not necessarily so; a pressure switch is but one way of automatically controlling a pump, float switches and time clocks are other methods commonly used. Some control boxes also contain motor capacitors which are essential parts of the pump motor, remote mounted; some boxes don't. I suggest you either employ the services of a competent electrician and/or obtain a wiring diagram from the pump/motor manufacturer. Good luck!

Correct, if you just connect the pump to the "box", I assume you mean the panelboard, the pump wll run continuously. Some pumps do go to a control box, that would contain a contactor (large relay) that is controlled by a pressure switch.

Small motors,1/2-3/4 HP may use just the pressure switch.

Rwm:
I don't think you shouls have disagrred with me because my reply started with "If". That means I didn't understand and should not be punished for it.

If it is an air switch, activate through lo, hi, off??
Continuity tester would verify switching, you may only need 2 connections on switch.
Is it 120 volts? Could need red or black reidentified as neutral. Yellow could be for a switch leg for a light. Can you see where the other end of the wires come from, in the house
(fuse panel, frond door switches?