The west-east terrain cross-section along ~150km of the northern part of Israel has a coastal-plain—mountain—valley structure; hereafter denoted iCMV. The boundary layer height (BLH) evolution mechanism across the iCMV has not yet been fully understood. We use Weather Research and Forecasting (WRF) simulations and ceilometer measurements to decipher the iCMV BLH evolution mechanism during the late summertime period of 5-14 September 2017, where the daily maximum BLH at the mountainous city of Jerusalem (JrM; 800m above sea-level) varies by ~1000m. We first verify the BLH, simulated by 5 model configurations (with 4 different BL schemes). The RMSE for the 3 best configurations are around 160 and 200m for the coastal and JrM areas, respectively. An analysis of the simulated daily BL evolution reveals a general mechanism. In the early morning, the up-slope flows and synoptic forcing interact to induce a surface flow convergence (SFC) zone. During a westerly (easterly) synoptic flow, the SFC is induced east (west) of JrM. Assisted by the inland propagating sea breeze front, the SFC is advected eastwards during the afternoon, until it collapses at the valley bottom. The SFC zone is accompanied by a substantial positive vertical-wind column and a locally-elevated BLH. The more western the morning-time SFC is, the more likely the elevated BLH will pass during midday through JrM, with a higher daily maximum BLH.  The exact dependence of the BLH evolution and the associated temperature and humidity variations upon the synoptic regime require further study.