PURPOSES : This study aimed to develop a quantitative structure property relationships (QSPR) model to predict the density from the molecular structure information of the asphalt binder AAA1, a non-full connected structure mixed with a total of 12 molecules. METHODS : The partial least squares regression (PLSR) model, which models the relationship between predictions and responses and the structure of these variables, was applied to predict the density of a binder with molecule descriptors. The PLSR model could also analyze data with collinear, noisy, and multiple dimensional independent variables. The density and additive-free AAA1 binder’s molecule systems generated by an asphalt binder’s molecules-related study were used to fit the PLSR model with the molecular descriptors produced using alvaDesc software. In addition to developing the relationship, a systematic feature selection framework (i.e., the V-WSP- and PLSR-modelbased genetic algorithm (GA)) was applied to explore sets of predictors which contributed to predicting the physical property. RESULTS : The PLSR model accurately predicted the density for the AAA1 binder’s molecules using the condition of the temperature and aging level (R2 was 0.9537, RMSE was 0.00424, and MAP was 0.00323 for the test data) and provided a set of features which correlated well to the property. CONCLUSIONS : Through the establishment of the physical property prediction model, it was possible to evaluate the physical properties of construction materials without limited experiments or simulations, and it could be used to comprehensively design the modified material composition.