The invention discloses a method and a system for controlling a variable output pump assembly, wherein the variable output pump assembly is formed by connecting n variable output pumps in parallel; according to a target output volume q of the variable output pump assembly, under a predetermined working pressure p, a functional relation between the efficiency e of the variable output pump assembly and the target outputs q1, q2, ellipsis, qn of the n variable output pumps is constructed; according to the functional relation, the target outputs q1, q2, ellipsis, qn of the n variable output pumps under the maximum efficiency max(e) of the variable output pump assembly is worked out through a optimization algorithm; and moreover, the n variable output pumps in the variable output pump assembly are controlled to run under the target outputs q1, q2, ellipsis, qn. In such a way, the efficiency and the service life of the variable output pump assembly are improved and prolonged respectively. The invention also provides engineering machinery comprising a control system of the variable output pump assembly.