The invention discloses an automatic winding machine and a winding method for a roll type membrane element protective net, and the automatic winding machine for the roll type membrane element protective net comprises a machine frame, a feeding system, a position system, a clamping system, a heating system and an auxiliary system; the heating system comprises a heater, a heater upper and lower driving device driving the upper and lower reciprocating motion of the heater, and a heater front and back driving device driving the front and back reciprocating motion of the heater; the auxiliary system comprises a clamping groove, a pressing plate parallelly arranged in the clamping groove, a clamping groove driving device driving the front and back reciprocating motion of the clamping groove, and a pressing plate driving device driving the front and back reciprocating motion of the pressing plate. The automatic winding machine semi automation equipment, by use of the automatic winding machine, only one person can complete winding of an outer protective net, the outer protective net is tightly wound, the production efficiency is high, the cost is low, the length of the heater is not shorter than the length of a to-be-processed membrane element, the thermal bonding process can be once completed, and the adhesion is rapid.