The invention discloses a method and a system for carrying out magnetic micromanipulation on a cell in a physiological environment. The system for carrying out the magnetic micromanipulation on the cell in the physiological environment comprises a magnetic probe, a probe nanometer offset detection module, a three-dimensional displacement platform, an inverted / upright optical microscope, a magnetic probe control module and a displacement control module and realizes the in-vitro operation and real-time tracking observation of a biological cell by being placed into a fine controlled culture environment suitable for the in-vitro growth of the cell. The method for carrying out the magnetic micromanipulation on the cell is characterized by measuring a single cell which contains magnetic nanometer particles point by point according to a selected area by utilizing the magnetic probe on the basis that the magnetic micromanipulation on the cell is combined with the magnetic nanometer particles, recording the magnitude of magnetic force, simultaneously acquiring the magnetic force and shape dot images at a nanometer scale and operating, moving, carrying, injecting and testing the single cell by using the magnetic probe by accurately positioning the magnetic cell and the magnetic nanometer particles, thereby achieving the guiding significance on a nanometer biological technology and micro-nanomanipulation technologies.