In a cross-scavenged two-stroke engine, a piston with a deflector is often utilized to flow the fresh charge toward the cylinder head and away from the exhaust port. But flow-visualization studies have shown that the fresh charge flows toward the cylinder head even without the deflector. To find why the fresh charge flows toward the cylinder head, we used Fluent, a general purpose computational fluid dynamics (CFD) software, to simulate two- and three-dimensional flows in a cross-scavenged two-stroke engine. While the fresh charge entered from the scavenging port into the cylinder and flowed across the cylinder, we investigated the instantaneous fresh charge flow, velocity, and pressure distribution in the cylinder. Results indicated that the fresh charge was forced toward the cylinder head by the “variable pilot vortex,” that is the vortex formed above the fresh charge flow, and by the “variable deflect pressure,” that is the higher pressure field formed in front of the flow immediately after the fresh charge flowed from the scavenging port to the cylinder. As the “variable deflect pressure” moved to the center of cylinder, it decreased and eventually disappeared. The “variable pilot vortex” and the “variable deflect pressure,” which act as natural and variable control deflectors, usefully cause the fresh charge to flow with an upward inclination.