The inter-storey drift limitations are meaningful reference values for structural seismic performance evaluation. This paper presents an analytical investigation into the seismic performance of multi-storey cross-laminated timber (CLT) structures to obtain the drift limitations under different earthquake hazard levels reasonably. The Pinching4 model was used to simulate the nonlinear mechanical behavior of three types of connections used in CLT structures, and a numerical model was further developed to capture the lateral load-resisting properties of CLT shear walls. Moreover, three benchmark multi-storey CLT apartment buildings were designed using the Equivalent Static Force Procedure according to National Building Code of Canada (NBCC), and simplified structural models were developed for these buildings. Depending on the results from numerous time-history dynamic analyses, the empirical cumulative distribution functions (CDFs) of the maximum inter-storey drifts were constructed for the three benchmark buildings. The probability of non-exceedance (PNE) of inter-storey drift thresholds under different earthquake hazard levels was proposed and validated. It is recommended that for low-rise CLT buildings within three stories, values of 0.30%, 0.75%, and 1.40% can be considered as the drift limitations for frequent, medium, and rare seismic hazard levels, respectively. For mid-rise or high-rise buildings without three stories, 0.25%, 0.70%, and 1.30% can be considered as drift limitations.