Ship collision risk is an important aspect of ship navigation safety. A systematic method to assess collision risk by monitoring parameter states continually is necessary and has proven effective. Another important factor in risk assessment is ship size, but the effect of the size of ship pairs has not been considered properly in many previous studies. This research utilises a systematic perspective to study collision risk of near-misses in ship-ship encounters. This fills a secondary research gap where previous risk assessments only investigated near-misses from the perspective of a single vessel. Following this proposed approach, ship pair encounter states can be continually tracked. Ultimately, a method of improved Vessel Collision Risk Operator (VCRO) to merge risk assessments of both ships is proposed through integration of near-miss collision risks in a systematic way, which overcomes the disadvantages of prior VCROs that only consider the maximum value, from which it is difficult to track and judge the risk trend. Utilising a case study, the effectiveness of the proposed method is validated through analysis of ship encounters, with ships of different sizes in the Baltic Sea.