The genesis of beryllium (Be) mineralization associated with granitic tin (Sn)- tungsten (W) deposit has received little attention, especially the fluid Be concentration variation along with the developing of skarn. For revealing the less-known skarn Be enrichment characteristics, in-situ electron probe microanalysis (EPMA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) along with element mapping were performed on the Be-bearing vesuvianite and scapolite grains from the Cuonadong Sn-W-Be skarn. As the main Be-bearing calc-silicate minerals, the vesuvianite (X19Y13Z18T0-5O68W10) and scapolite (M4T12O24A) incorporate Be element via occupying normally vacant T site and the Al-2(SiBe) substitution, respectively, and show outward increased Be content related to the varying solid-solution composition arising from the dynamic evolution of skarn. The homogeneous core enveloped by oscillatory mantle and rim under BSE or CL image and the increased liquid inclusion size towards the rim reflect both mineral’s staged growth under an elevated water–rock ratio. The increased Ca activity caused by enhanced interaction between fluid and Mn-containing carbonate may drive scapolite constituent change through (NaSi)-1(CaAl) substitution, creating more tetrahedral Al sites suitable for Be occupation and resulting in the increased Ca, CO32–, Be content and decreased Na content from core to rim. Precipitation of fluorite will lead to a reduce in hydrothermal Be solubility associated with a decreased fluorine activity, and favor Be to occupy the vacant T site by losing more hydrogen from the anion W site and finally form the Be-rich, Ca- and F-low vesuvianite rim. Significantly high Be, Sn, Mn and low Sr, LREE, U content at vesuvianite rim along with hydration alteration and mineralization suggest the onset of retrograde stage. Overall, the dynamic growth and epitaxially rising Be concentration of vesuvianite (∼97–1032 ppm) and scapolite (∼902–2928 ppm) recorded that the later pulsed fluid enriched Be as skarn developed, implying high grade Be mineralization tends to occur in the late magmatic-hydrothermal stage for F-rich peraluminous magmatic system.