Fluorescence　fluctuation-based　super-resolution　microscopy　is　a　cost-effective　and　widely　applicable　super-resolution　microscopic　technology,　which　has　broad　applications　in　observing　subcellular　structures　and　monitoring　their　kinetic　processes.　However,　it　is　highly　demanded　to　systematically　study　the　reconstruction　quality　of　various　fluctuation-based　superresolution　algorithms　under　different　fluorescence　temporal　fluctuations.　In　this　paper,　firstly,　the　performances　in　the　image　quality　of　multiple　algorithms　under　different　conditions　are　quantitatively　analyzed　and　compared　by　employing　various　evaluation　metrics　such　as　Resolution　Scaled　Pearson＇s　coefficient　(RSP),　Resolution　Scaled　Error　(RSE),　Signal-to-Noise　Ratios　(SNRs),　Relative　error　of　strength　(K),　and　Resolution　(R).　Then,　a　comprehensive　evaluation　factor　(CEF)　was　defined　by　combining　5　parameters　for　the　evaluation　of　all　algorithms,　and　the　advantages　and　applicable　conditions　of　various　algorithms　are　summarized　and　analyzed.　Furthermore,　this　paper　establishes　a　general　model　using　a　multi-layer　perceptron　(MLP)　to　accurately　predict　the　most　suitable　super-resolution　algorithms　under　different　conditions.　In　addition,　a　software　platform　for　multi-algorithm　fluorescence　fluctuation　super-resolution　nanoscopy　was　developed,　which　can　realize　the　generation　of　fluorescence　fluctuation　signals,　synchronize　multiple　super-resolution　algorithms,　and　the　evaluation　of　reconstructed　images.　The　results　show　that　high-quality　super-resolution　images　can　be　obtained　by　increasing　image　frames　together　with　enhancing　the　fluorescence　fluctuation　signals.　The　model　of　the　multilayer　perceptron　performs　well　with　high　output　accuracy　(＞95%)　after　multiple　iterations　of　training　and　exhibits　good　prediction　capability　that　can　reduce　additional　experiments　and　improve　experimental　efficiency.　These　studies　will　facilitate　the　implementation　of　fluctuation-based　super-resolution　techniques　for　the　research　of　subcellular　organelle　investigation　under　various　fluorescent　labeling　conditions.　©　2024　IEEE.