The first Abbot of Shaolin Monastery was Batuo (also called Fotuo or Buddhabhadra, not to be confused with Bodhidharma) was a dhyana master who came to China from India in 464 AD in order to spread Buddhist teachings.

According to the Continued Biographies of Eminent Monks (645 AD), the Shaolin Monastery was built on the north side of Shaoshi, the central peak of Mount Sung, one of the Sacred Mountains of China, by Emperor Xiaowen of the Northern Wei Dynasty in 477 AD. Kangxi, the second Qing emperor, was a supporter of the Shaolin temple in Henan and he wrote the calligraphic inscriptions that hang over the Heavenly King Hall and the Buddha Hall to this day.

The monastery has been destroyed and rebuilt many times. In 1641 the troops of an anti-Ming rebel, Li Zicheng sacked the monastery due to the monks' support towards the Ming and the possible threat they posed to the rebels. This destroyed the temple's fighting force.Perhaps the most-known story of the Temple's destruction is that of it’s destraction by the Qing dynasty for supposed anti-Qing activities. Although this destruction is also known for helping Shaolin martial arts spread through China by means of the five fugitive monks.

In1928, the warlord Shi Yousan set fire to the monastery, burning it for over 40 days, destroying 90 percent of the buildings including many manuscripts of the temple’s library.

The Cultural Revolution launched in 1966 targeted religious orders including the monastery. The five monks who were present at the monastery when the Red Guard attacked were shackled and made to wear placards declaring the crimes charged against them. The monks were jailed after publicly being flogged and paraded through the street as people threw rubbish at them. The government purged all Buddhist materials from within the monastery walls, leaving it barren for years.