It is easier for blood to love down your body rather than up due to gravity. The veins and arteries in your feet are used to this and so are good at coping with the amount of blood they get. When you stand on your head, it increases the flow of blood to your head. The throbbing you feel is, I think, the beating of your heart increasing the pressure in the blood, which you can feel more clearly due to all the extra blood filling your head!
Its all about blood pressure. It takes more pressure to pump blood into the brain because it is at a higher elevation than the heart than to the legs which are lower and can take advantage of gravity. If you are standing on your head, you are adding the effect of gravity to the pressure exerted by the heart and more blood flows through your head making it throb. The throbbing is a pulse in your head like the one on your wrist. It is the blood flowing through valves in the blood vessels which stop the blood flowing backwards.