A fuel injector is disclosed. The fuel injector may have an injector body having a fuel inlet and at least one orifice. The fuel injector may also have a first check valve member. The first check valve member may be selectively movable to fluidly block a first flow of fuel from the fuel inlet to the at least one orifice. The fuel injector may have a second check valve member. The second check valve member may be selectively movable to fluidly block a second flow of fuel from the fuel inlet to the at least one orifice. The fuel injector may also have a control valve assembly. The control valve assembly may be configured to selectively operate either the first check valve or both the first check valve and the second check valve to fluidly connect the fuel inlet and the at least one orifice.