The retail giant has faced growing opposition in China since signing a deal to provide land for a US missile-defence system Tuesday.
The plan to install the Terminal High-Altitude Area Defense (THAAD) system was prompted by threats from North Korea, but Beijing fears the move will undermine its own military capabilities.
"No to THAAD! Boycott Korean goods!" chanted the protesters in northern Jilin province.
"Patriotism starts with me! Long live the Communist Party!"
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Citing fire violations, authorities in Liaoning's Dandong city have also suspended the operation of Lotte Mart, the Yonhap news agency reported on Saturday.
Earlier this week, major tour operators confirmed to AFP that trips to South Korea have been suspended "due to policy and safety factors."
China has repeatedly denounced THAAD as a threat to its security, with a foreign ministry spokesman saying "the consequences entailed will be borne by the US and the Republic of Korea".
The stakes are high for Lotte, which has invested more than ten trillion won ($8.76 billion) in its Chinese operations since 1994.