How to calculate the speed of a motorcycle weight about 330kg hitting a man of 60kg and throwing him to a distance of 3 meters? In normal road circumstances.

This is imposible to calculate from fundamental physics - there are too many variables that would affect the result. You would have to run the experiment multiple times to see what results you get, to understand the effects of variables such as whether the motorcycle hit the man square on or with a glancing blow, where in his body was he struck, and was the man stationary or walking across, toward, or away from the motorcycle. Other factors to be considered are whether the man fell onto the handle bars and was carried forward a bit before falling off, and did he roll after hitting the ground. I would bet that the police accident investigators proably have some guidelines they use to estimate the impact speed in cases like this. Perhaps the most telling bit of evidence would be the amount of damage to the motorcycle.