Joint prevention and control of atmospheric pollution is an effective approach to facilitating effective control of atmospheric pollution and improving regional air quality. Based on regional public product attribute of atmospheric pollution control, the paper takes the Yangtze River Delta for example to establish an cross-regional atmospheric pollution collaborative governance system and proposes a number of system operation principles: regarding diverse control entities as foundation, regarding motivation of control entities as the key factor, regarding collaborative mechanism innovation and improvement as the root and regarding external environment optimization as the guaranteer.