The invention discloses an HHT (Hilbert-Huang Transform)-based harmonic detection system for a grid-connected inverter of a photovoltaic system. The HHT-based harmonic detection system comprises a signal acquiring and preprocessing circuit unit, an analog-digital conversion circuit unit, a main control unit, an SRAM (Static Random Access Memory) unit, a CPLD (Complex Programmable Logic Device), a dual-port RAM (Random Access Memory) unit, a communication unit, a micro control unit, a display unit and an input unit. A working method comprises the steps of current signal acquisition, conversion, filtering, processing, frequency splitting and judging. The HHT-based harmonic detection system has the advantages that (1) a hardware device is simple and practical; (2) high measuring accuracy is achieved; (3) high instantaneity is realized; (4) high system compatibility is realized; (5) power quality of a power grid is improved.