To measure the 3D microdisplacement of a self-oscillating polymer gel driven by the Belousov-Zhabotinsky reaction, we propose, to the best of our knowledge, a new particle detection and tracking method based on a phase image/volume template matching using digital holographic microscopy. We demonstrate the precision of the proposed method and compare it with conventional approaches. The method is applied to 3D measurement of the motions of particles attached to the surface of an oscillating gel. Measurement results show that the local area of the gel oscillates periodically, and the motion propagates throughout the gel. Our method can measure rapid and complex 3D microdisplacement change.