The invention discloses a 3D shape detection system and method. The system comprises an automatic objective table, an optical microscopic imaging system with longitudinal chromatic aberration, a narrowband multispectral image sensor with a channel quantity N being greater than or equal to 4, a control unit and an image analysis unit, wherein the objective table is connected with the control unit,the image analysis unit is electrically connected with the multispectral image sensor and the control unit, and the optical microscopic imaging system is mechanically connected with the multispectralimage sensor. Via the 3D shape detection system and method, a plurality of narrowband spectral images capable of natural calibration of XY spatial positions of object surfaces and different in focusing definition can be obtained via one single exposure. By using a matching defocus ambiguity algorithm and a matching autofocus method, 3D shapes of the object surfaces, namely depth Z information of any spatial position XY, can be obtained in a full automatic way; the system and the method disclosed in the invention can be widely applied to rapid online detection of surface shapes of advanced manufactured cutters, precision samples or parts.