The invention discloses a low-cost large-field functional-molecular-structural imaging system and method aiming at medical isotope. The system comprises a functional-molecular-structural imaging coaxial detector, a data processing device and a computer device, wherein the functional-molecular-structural imaging coaxial detector is used for scanning a physical imaging object to obtain the functional and molecular imaging image information and structural imaging image information of the physical imaging object and outputting the information to the data processing device; the data processing device is used for receiving and storing the functional and molecular image information and decomposing the structural information, carrying out fusion calculation on the functional-structural images, drawing a multi-modality fused section image, and transmitting the image to the computer device for displaying; and the computer device is used for realizing image reconstruction and displaying the functional-molecular-structural multi-modality fused section image. According to the invention, a charge-coupled device and spiral CT (computerized tomography) are adopted for detecting effective information at coaxial aperture position, thus as compared with PET (positron emission tomography) / CT, SPECT (single photon emission computed tomography) / CT and other bi-modality imaging devices, the imaging axial-direction field is enlarged, the whole body imaging time is shortened, and the isotope imaging cost is greatly lowered.