Saint Patrick according to the legend used shamrock to explain the concept of Trinity in Christianity meaning the Father, the Son and the Holy Spirit. As the shamrock is three leafed clover and the Trinity also has three elements, this similarity was used by him in 5th century to explain the doctrine to pagan Irish.
Saint Patrick is fifth century Irish bishop. He used shamrock to represent the Christian Doctrine of Holy Trinity. It was the time of Christianising of Ireland. Indeed, three was an important deity in Pagan Ireland and Saint Patrick used it as a reliable effort. In the attached picture you can see him holding shamrock in his right hand on the glass window of Saint Benin's church of Ireland.
