In the conventional femtosecond laser direct writing with a Gaussian beam, the focus is an ellipsoid with the long axis along the beam propagation direction, resulting in the ellipsoidal fabricated dot. Due to the simple shape of the dot, complex three-dimensional (3D) nano/microstructures should be written dot by dot by the focus scanning, which is usually time-consuming. Therefore, a rapid nano/microfabrication technique is becoming highly desired to achieve arbitrary 3D nano/microstructures. By 2D phase modulation of the Gaussian beam, multi-focuses were generated for the direct writing of several same nano/microstructures simultaneously to save fabrication time, and donut and other 2D intensity distributions were produced for the single exposure fabrication of 2D microstructures. Here, we demonstrate the single-exposure two-photon polymerization of a 3D microstructure via the 3D focal field engineering by using the 2D phase-only spatial light modulation. With a single exposure, a whole 3D microstructure like a double-helix is polymerized simultaneously, whose configuration is controlled by the designed 3D focal intensity distribution. In addition, a longitudinal circular intensity distribution is generated for the multi-photon inscription of a depressed cladding waveguide inside glass with single scan transverse writing.