The invention provides a method for comprehensively treating copper oxide ore with high contents of mud, iron, calcium and magnesium, which comprises the steps of ore washing, acid heap leaching and acid agitation leaching, wherein the ore washing comprises the steps of: A, performing mud removal on lump and powdered mixed ore through first-grade ore washing, and obtaining clean lump and grained ore with a particle size of over +5mm and mud-intercalated ore with a particle size of below -5mm through screening; B, sending the cleaned lump and grained ore with a particle size of over +5mm to a heap leaching field, and performing secondary scrubbing on the mud-intercalated ore with a particle size of below -5mm to obtain placer with a particle size of between +1 and -5mm and mud ore with a particle size of below-1mm through screening; and C, sending the placer with a particle size of between +1 and -5mm to the heap leaching field, and sending the mud ore with a particle size of below -1mm to an agitation leaching working procedure. The method saves ore grinding equipment with higher energy consumption, can also fully play respective mineral dressing advantages of heap leaching and agitation leaching, and radically solve the problem that conventional lump and powdered mixed copper oxide fails to be leached, reduces the product cost, more importantly, does not discharge any contaminating fluid to the external world, and is favorable for protecting production and surrounding environments.