Five-axis hybrid machine tools are widely used due to the advantages of high speed, high precision, and good performance in the aviation and aerospace manufacturing industry. Many scholars have studied the basic theories and key technologies along with the widespread attention of academia and industry thereon. An integrated geometric error modelling method, under the unified coordinate system framework for a general five-axis hybrid machine tool based on a 3-PRS parallel spindle head, is proposed. The kinematic inverse model of a hybrid machine tool is built using a vector chain method. On the basis of the analysis of the various error sources, an integrated geometric error model is developed based on perturbation theory. Then, the influence of each error source of a hybrid machine tool is investigated at the end-effector. Screw theory is applied to research error source separation for the 3-PRS parallel spindle head of a hybrid machine tool, and a sensitivity analysis of the error sources is undertaken using statistical methods. Based on this, the compensable error sources and non-compensable error sources of a hybrid machine tool are separated successfully. The non-compensable error sources must be strictly controlled in the process of design and manufacture, while the compensable error sources can be compensated inexpensively by software after reaching some degree of accuracy in the design and manufacture. This research provides a theoretical reference for this kind of machine tool design and its use in manufacturing.