Background: Preconception care (PCC) is recommended for optimizing a woman’s health prior to pregnancy to minimize the risk of adverse pregnancy and birth outcomes. We aimed to evaluate the impact of strategy and a novel risk classification model of China´s “National Preconception Health Care Project” (NPHCP) in identifying risk factors and stratifying couples’ preconception health status. Methods: We performed a secondary analysis of data collected by NPHCP during April 2010 to December 2012 in 220 selected counties in China. All couples enrolled in the project accepted free preconception health examination, risk evaluation, health education and medical advice. Risk factors were categorized into five preconception risk classes based on their amenability to prevention and treatment: A-avoidable risk factors, B- benefiting from targeted medical intervention, C-controllable but requiring close monitoring and treatment during pregnancy, D-diagnosable prenatally but not modifiable preconceptionally, X-pregnancy not advisable. Information on each couple´s socio-demographic and health status was recorded and further analyzed. Results: Among the 2,142,849 couples who were enrolled to this study, the majority (92.36%) were from rural areas with low education levels (89.2% women and 88.3% men had education below university level). A total of 1463266 (68.29%) couples had one or more preconception risk factors mainly of category A, B and C, among which 46.25% were women and 51.92% were men. Category A risk factors were more common among men compared with women (38.13% versus 11.24%; P = 0.000). Conclusions: This project provided new insights into preconception health of Chinese couples of reproductive age. More than half of the male partners planning to father a child, were exposed to risk factors during the preconception period, suggesting that an integrated approach to PCC including both women and men is justified. Stratification based on the new risk classification model demonstrated that a majority of the risk factors are avoidable, or preventable by medical intervention. Therefore, universal free PCC can be expected to improve pregnancy outcomes in rural China.