The problem of generalised minimum variance control of linear multi-input multi-output time-varying systems is studied. The plants are described using a time-varying controlled autoregressive moving average model and the cost functional is the sum of plant output tracking error variances plus squared control variables. Both the output errors and the input variables are weighted using time-varying matrices. A generalised minimum variance controller is developed in a transfer operator framework without using a pseudocommutation technique. The minimum variance controller is extended and the stably invertible condition is removed for multi-input multi-output time-varying systems. The controller can be applied to a large class of linear time-varying stochastic systems.