Southerners had a stronger fighting spirit than northerners because
they were fighting for independence.
they were fighting to end slavery.
northerners had a smaller army.
northerners did not care about the union.

They were fighting for independence.  Many of soldiers from the South had deep roots in their states.  Many felt strongly about defending their rights and believed the Union was interfering with their rights. Still, the North had more manpower and industry.  When Generals like Grant, Sheridan and Sherman came along, the North turned the tide and won the war.