The invention discloses a processing system of human body health data and a method thereof. The processing system comprises an acquisition unit, a first processing unit, a second processing unit, a computing unit and an output unit. The acquisition unit is used for obtaining physical sign data of healthy state of an individual through an APP application; the first processing unit is used for carrying out healthy features construction on the physical sign data by using a vector space modal; the second processing unit is used for extracting features, constructing a data set, and detecting denoising and reconstitution of the data through the features; the computing unit is used for digging and determining healthy impact factors which impact the corresponding individual; the output unit is used for generating a healthy analysis result of the corresponding individual as well as information about guidance and suggestions. The processing system of human body health data and the method thereof have the advantages that through techniques such as data automatic detection, mobile computing, information extraction, association digging, neutral network and machine learning, determining individual health state and developmental tendency from individual health data, conducting continuously trailing and real-time warning, analyzing healthy impact factor, promoting individual health level, carrying out prevention before disease onset, preventing disease from exacerbating and guiding the individual to adopt a most appropriate health behavior. The processing system of human body health data and method thereof are very convenient to realize.