Magnetic skyrmions are topologically protected spin configurations and have recently received growingly attention in magnetic materials. The existence of biskyrmions within a broad temperature range has been identified in our newly-discovered MnNiGa material, promising for potential application in physics and technological study. Here, the biskyrmion microscopic origination from the spin configuration evolution of stripe ground state is experimentally identified. The biskyrmion manipulations based on the influences of the basic microstructures and external factors such as grain boundary confinement, sample thickness, electric current, magnetic field and temperature have been systematically studied by using real-space Lorentz transmission electron microscopy. These multiple tuning options help to understand the essential properties of MnNiGa and predict a significant step forward for the realization of skyrmion-based spintronic devices.