Well actually it isn’t a secret - it is in fact the Toyota Production/Management System. Maybe, if people assume the TPS is about improvement in the factory alone, then they could miss the true importance as the management system that it is. So I quibble a little bit with the title but this is actually a good article by John Teresko, Toyota’s Real Secret: Hint, It’s Not TPS:

To me saying the Toyota Production System is only about manufacturing is like saying “lean manufacturing” is only about manufacturing. The article is certainly correct in stating that moving the thought process to a systems view that incorporates the entire system is key - as Dr. Deming said in 1950 and I think Toyota has understood perfectly well for decades. Maybe I am being sloppy in not separating TPS from Toyota Management but I think most people think of TPS as Toyota’s overall management system.