Introduction: This study aimed to investigate the baseline level of malaria awareness in residents in 20 malaria-endemic provinces from October 2010 to January 2011 at the beginning of the implementation of the China National Malaria Elimination Programme (NMEP). Methodology: A structured questionnaire about basic malaria knowledge was administrated to residents in rural areas from 20 provinces, municipalities, and autonomous regions. Results: A total of 182,085 residents no younger than 15 years of age took part in the cross-sectional investigation; 3,232 were excluded because of incomplete survey responses. Of the respondents, 56.86% were aware of malaria, 18.03% responded correctly to all five questions, and 5.57% answered all the questions incorrectly. Malaria awareness among different age groups was statistically significant (p < 0.001), males had a better understanding of malaria than did females (p < 0.001), and Type I counties had a better understanding than did Type II counties (p < 0.001). Conclusions: The level of malaria awareness was low among residents at the beginning of the NMEP, especially about malaria pathogenicity and preventive methods. Health education campaigns should be developed and implemented to increase the public perceptions about malaria prevention and treatment, and to promote malaria elimination in China.