Background This study aimed to develop a new scoring system for predicting recurrent thrombosis in patients with antiphospholipid syndrome (APS). Methods This was a retrospective multicentre cohort study. Patients with APS were followed up from APS diagnosis to either recurrent thrombosis or their last follow-up date, whichever came first. A multivariable logistic regression analysis with a backward elimination was used to develop a new scoring system, incorporating conventional cardiovascular risk factors and antiphospholipid antibody (aPL) profile as covariates. Each covariate remaining in the final step was multiplied by its (3 coefficient, rounded to the nearest integer, and then summed. A multivariable Cox proportional hazard model, adjusted for medication use, assessed the association between the new scoring system and recurrent thrombosis risk. The accuracy of the new scoring system in predicting recurrent thrombosis was evaluated by estimating the area under the curve (AUC) and comparing it with the adjusted global APS score (aGAPSS). Results A total of 126 patients with APS were included. The median age of the cohort was 40 (interquartile range: 31-55) years and 49.2% were women. Hypertension, type 2 diabetes mellitus (T2DM), and dyslipidaemia were present in 20.6%, 18.3%, and 54.0% of the patients, respectively. 26.2% were current smokers and 23.8% had concomitant systemic lupus erythematosus. Lupus anticoagulant (LA), anti-(32 glycoprotein I (anti-(32GPI) IgG, anti-(32GPI IgM, anticardiolipin (aCL) IgG, and aCL IgM were positive in 76.2%, 27.0%, 11.9%, 27.0%, and 6.3% of the patients, respectively. During a median follow-up duration of 41.5 (interquartile range: 21.4-72.0) months, thrombosis recurred in 9 (7.1%) patients. Multivariable logistic regression analysis revealed the following scoring system: modified diabetes global APS score (mdGAPSS)= 1*T2DM +2*LA +1*anti-(32GPI. Multivariable Cox proportional hazard model showed that a higher score was significantly associated with an increased risk of recurrent thrombosis (adjusted hazard ratio 2.911, 95% confidence interval 1.090-7.770, p = 0.033).The AUC was higher using the mdGAPSS (AUC = 0.706) than the aGAPSS (AUC = 0.553). Conclusions Compared to the aGAPSS, the mdGAPSS-comprising T2DM, LA, and anti-beta 2GPI-demonstrated a greater accuracy in predicting recurrent thrombosis in patients with APS.