Specialist police stormed the clandestine laboratory at a property in Horning Street, Kurnell about 5pm on Thursday after months of investigations into the drug operation.
Two men, aged 56 and 29, were arrested at the scene and taken to Sutherland Police Station.
About six kilograms of MDMA and more than 100kg of drug and precursor chemicals were found alongside hundreds of pieces of lab equipment inside a shed a the back of the property.
Almost $200,000 cash was also found.
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The older man was charged with manufacturing a large commercial quantity of a prohibited drug.
The younger man was charged with taking part in the manufacture of a large commercial quantity of a prohibited drug.
Both men were refused bail before Sutherland Local Court and are next due to appear before Downing Centre Local Court in July.
Anyone with information about the supply and manufacture of illicit drugs is urged to contact police.