To cut down immense greenhouse gases emission and energy consumption in the rapidly urbanizing world, a holistic understanding and rethinking of our dynamic urban energy system are inevitable. Performing bottom-up building energy modelings at urban scale based on Geographic Information System (GIS) and semantic 3D city models could be a promising option to provide quantitative and integrated energy solutions. Nevertheless, input uncertainties either caused by limited data accessibility in most cities or parameters with stochastic variability (e.g. house occupancy profile) become one of the biggest obstacles to produce reliable and acceptable building energy modeling results. This study aims to address the heating demand simulation performance gap caused by input uncertainties. In this case study based on Amsterdam residential building stock, parameter importance ranking of the 14 simulation inputs are first derived according to the sensitivity analysis. The selected key uncertain parameters are then modeled in a probabilistic distribution way at postcode 6 level (approximately or slightly more than 10 buildings). Model calibration is based on the Bayesian approach and given six years (2010-2015) of gas consumption data to infer parameter posterior distributions. After the training phase, the calibrated annual heating demand simulation results of the validation years show significant improvement in modeling accuracy. Comparing the baseline and the calibrated simulation results, the averaged absolute percentage errors of energy use intensity (EUI) among at least 84 valid postcodes have decreased from 24.96% to 8.31% in 2016 and from 19.93% to 7.70% in 2017 respectively. The calibrated urban building energy model would be most interested by municipalities, urban planners, and engineering consultancies. It can be used to evaluate long-term energy supply and demand strategies, identify building renovation saving potential, perform large-scale building performance mapping, and carry out retrofit measures assessment.