The invention provides a coal uncovering outburst prevention operation procedure for a tunnel which continuously and repeatedly penetrates coal seams on the complex structure conditions. The operationprocedure comprises the following steps that first, a security assurance system is built; second, regional comprehensive outburst prevention measures are taken, wherein the regional comprehensive outburst prevention measures include advance geology forecast, regional outburst risk forecast, regional outburst prevention measures, regional measure effect tests and regional verification; third, local comprehensive outburst prevention measures are taken, wherein the local comprehensive outburst prevention measures include working surface forecast, working surface measures, working surface outburst prevention effect tests and security assurance measures; and fourth, coal is uncovered. The coal uncovering outburst prevention operation procedure for the tunnel which continuously and repeatedly penetrates the coal seams on the complex structure conditions is based on quaternity of the regional comprehensive outburst prevention measures and the local comprehensive outburst prevention measures;and in the circumstances that security assurance system is implemented against gas outburst beforehand in a multidirectional manner, comprehensive advance geology forecast, the regional forecast, suction and exhaust, and verification which are included in the comprehensive outburst prevention measures and the local comprehensive outburst prevention measures are implemented for the tunnel to penetrate all the coal seams at one time, and it is effectively guaranteed that coal uncovering is safe to carry out when the tunnel penetrates gas outburst layers continuously and repeatedly on the complex structure conditions.