diff --git a/apps/web/vue3/index.html b/apps/web/vue3/index.html
index 209f8a75b..8711554d2 100644
--- a/apps/web/vue3/index.html
+++ b/apps/web/vue3/index.html
@@ -20869,18 +20869,25 @@ compare: [[flesh, peel]]`;
                         if (!response.ok) throw new Error(await extensionApiError(response, '文件上传失败'));
                         const data = await response.json();
                         const uploaded = (data.files || []).map(name => `input/${jobId}/${name}`);
-                        const targetInput = lightweightNlRun.inputs.find(item => !String(item.value || '').trim()) || lightweightNlRun.inputs[0];
-                        if (targetInput) {
-                            targetInput.value = uploaded.shift() || '';
-                            const rest = uploaded.filter(Boolean);
-                            if (rest.length) {
-                                const emptyInputs = lightweightNlRun.inputs.filter(item => !String(item.value || '').trim());
-                                for (let i = 0; i < rest.length && i < emptyInputs.length; i++) {
-                                    emptyInputs[i].value = rest[i];
-                                }
+                        // 优先按文件名与输入槽名精确匹配填入，避免把序列文件误填进 samples.tsv 等槽位
+                        const remaining = [...uploaded];
+                        for (const input of lightweightNlRun.inputs) {
+                            if (String(input.value || '').trim()) continue;
+                            const slotName = String(input.key || '').trim().toLowerCase();
+                            const hitIndex = remaining.findIndex(path => {
+                                const base = String(path || '').split('/').pop().toLowerCase();
+                                return slotName && (base === slotName || base.endsWith('.' + slotName));
+                            });
+                            if (hitIndex >= 0) {
+                                input.value = remaining.splice(hitIndex, 1)[0];
                             }
                         }
-                        ElMessage.success(`已上传 ${uploaded.length} 个文件`);
+                        const emptyInputs = lightweightNlRun.inputs.filter(item => !String(item.value || '').trim());
+                        for (let i = 0; i < remaining.length && i < emptyInputs.length; i++) {
+                            emptyInputs[i].value = remaining[i];
+                        }
+                        const matched = uploaded.length - remaining.length;
+                        ElMessage.success(`已上传 ${uploaded.length} 个文件${matched ? `，已自动匹配 ${matched} 个输入槽` : ''}`);
                     } catch (err) {
                         ElMessage.error(err.message || '文件上传失败');
                     } finally {