This paper presents an investigation of the unsteady three-dimensional flow in an overexpanded rocket nozzle during a shutdown transient. Experimental and numerical investigations were carried out. It is known that, in some cases, an asymmetric flow induces a serious lateral force called “side load” during transient operations. The focus of the present study is to clarify characteristics of the asymmetric flow patterns. Results obtained by measurements and computations for the cases of the shutdown transient have shown qualitative agreement. The flow pattern becomes asymmetric during the transition of the separation pattern from restricted shock separation (RSS) to free shock separation (FSS). As a result, a large and impulsive side load was observed. Additionally, during the transition of the separation pattern, a three-dimensional vortex structure appeared on the nozzle wall in a separation bubble.