The present invention provides a system for recovering protein in a production process of an ultrahigh maltose syrup, including a saccharification tank, an enzyme preparation tank, a first plate heat exchanger, a second plate heat exchanger, a plate and frame filter, a buffer tank and a rotary drum filter. The present invention further provides a method of recovering protein by using the system. After the sugar liquid in the saccharification tank is stood, the protein floats at the upper part of the saccharification tank and the lower liquid is clear and transparent and thus the sugar liquid can be directly filtered. When the saccharification tank is discharged, the lower liquid is firstly discharged with the remaining liquid being bottoms containing protein. During a production process, enzymatic hydrolysis is performed for the sugar liquid containing protein before filtration to improve the filtration effect of the sugar liquid. Assisted by the plate and frame filter, protein can be recovered. The present invention improves the economic benefits, reduces the production costs, and thus solves the problem of difficulty in recovering protein in a production process of an ultrahigh maltose syrup.