The invention provides a nuclear power station thermal energy efficiency monitoring and diagnosing system and method. The monitoring and diagnosing system comprises a storage module, a data acquisition module, a core calculation module, and a diagnosis module. The data acquisition module is used for obtaining nuclear power station secondary circuit basic parameters measured by a monitoring system instrument and process parameters of a distributed control system; the core calculation module is used for calculating measured values of thermal power performance parameters of the nuclear power station secondary circuit, wherein an energy efficiency calculation model of the nuclear power unit is established on the basis of an energy efficiency distribution matrix equation established for the nuclear power station secondary circuit, and the unit specific heat consumption of the nuclear power station secondary circuit is calculated; the diagnosis module is used for determining whether the thermal power performance parameters are abnormal or not by comparing the measured values of thermal power performance parameters of the nuclear power station secondary circuit with operational reference values. According to the system and method, an energy efficiency distribution matrix equation is established for the nuclear power station secondary circuit; indexes such as unit specific heat consumption are obtained through establishing the energy efficiency calculation mode; and therefore a set of thermal energy efficiency monitoring index system is developed for a nuclear power station.