An apparatus and method for managing health data through a user terminal are provided. The method includes inputting a user terminal number for identifying the user terminal, and information of a medical instrument for measuring the health data to a management server interworked with the user terminal, receiving, by a receiver, a security type table mapped onto the user terminal number and comprising a security type code for instructing the health data which the medical instrument has measured to be stored in a first memory without security or in a second memory with security, from the management server, and storing the health data in the first memory or the second memory, which the security type code instructs, through determining the security type code of the security type table when the health data is received from the medical instrument.