The garden was planted at Valley Primary Academy, in Norwich, in memory of Summer Grant.
Summer, 7, died in March 2016 when the bouncy castle she was on in Harlow, Essex was blown away in high winds.
Norfolk Police said the three males were questioned and they were looking for a fourth male.
CCTV footage from the school showed four youths trashing the garden.
The force said the vandals also ransacked the school's reception class play area.
Three young men who trashed a memorial garden dedicated to a girl who died in a bouncy castle accident have been identified.