diff --git a/lld/ELF/LinkerScript.cpp b/lld/ELF/LinkerScript.cpp
--- a/lld/ELF/LinkerScript.cpp
+++ b/lld/ELF/LinkerScript.cpp
@@ -644,6 +644,20 @@
   for (OutputSection *sec : v) {
     if (sec->partition != isec->partition)
       continue;
+
+    if (config->relocatable && (isec->flags & SHF_LINK_ORDER)) {
+      // Merging two SHF_LINK_ORDER sections with different sh_link fields will
+      // change their semantics, so we only merge them in -r links if they will
+      // end up being linked to the same output section. The casts are fine
+      // because everything in the map was created by the orphan placement code.
+      auto *firstIsec = cast<InputSectionBase>(
+          cast<InputSectionDescription>(sec->sectionCommands[0])
+              ->sectionBases[0]);
+      if (firstIsec->getLinkOrderDep()->getOutputSection() !=
+          isec->getLinkOrderDep()->getOutputSection())
+        continue;
+    }
+
     sec->recordSection(isec);
     return nullptr;
   }
@@ -658,7 +672,8 @@
   StringMap<TinyPtrVector<OutputSection *>> map;
   std::vector<OutputSection *> v;
 
-  auto add = [&](InputSectionBase *s) {
+  std::function<void(InputSectionBase *)> add;
+  add = [&](InputSectionBase *s) {
     if (!s->isLive() || s->parent)
       return;
 
@@ -671,13 +686,17 @@
 
     if (OutputSection *sec = findByName(sectionCommands, name)) {
       sec->recordSection(s);
-      return;
+    } else {
+      if (OutputSection *os = addInputSec(map, s, name))
+        v.push_back(os);
+      assert(isa<MergeInputSection>(s) ||
+             s->getOutputSection()->sectionIndex == UINT32_MAX);
     }
 
-    if (OutputSection *os = addInputSec(map, s, name))
-      v.push_back(os);
-    assert(isa<MergeInputSection>(s) ||
-           s->getOutputSection()->sectionIndex == UINT32_MAX);
+    if (config->relocatable)
+      for (InputSectionBase *depSec : s->dependentSections)
+        if (depSec->flags & SHF_LINK_ORDER)
+          add(depSec);
   };
 
   // For futher --emit-reloc handling code we need target output section
@@ -685,6 +704,12 @@
   // to create target sections first. We do not want priority handling
   // for synthetic sections because them are special.
   for (InputSectionBase *isec : inputSections) {
+    // In -r links, SHF_LINK_ORDER sections are added while adding their parent
+    // sections because we need to know the parent's output section before we
+    // can select an output section for the SHF_LINK_ORDER section.
+    if (config->relocatable && (isec->flags & SHF_LINK_ORDER))
+      continue;
+
     if (auto *sec = dyn_cast<InputSection>(isec))
       if (InputSectionBase *rel = sec->getRelocatedSection())
         if (auto *relIS = dyn_cast_or_null<InputSectionBase>(rel->parent))
diff --git a/lld/test/ELF/relocatable-linkorder.s b/lld/test/ELF/relocatable-linkorder.s
new file mode 100644
--- /dev/null
+++ b/lld/test/ELF/relocatable-linkorder.s
@@ -0,0 +1,25 @@
+// REQUIRES: x86
+// RUN: llvm-mc %s -o %t.o -filetype=obj --triple=x86_64-unknown-linux
+// RUN: ld.lld %t.o -o %t -r
+// RUN: llvm-readelf -S %t | FileCheck %s
+
+// Test that SHF_LINK_ORDER sections with different linked sections
+// aren't merged.
+
+.section .text.f1,"ax",@progbits
+.globl f1
+f1:
+ret
+
+.section .text.f2,"ax",@progbits
+.globl f1
+f2:
+ret
+
+// CHECK: foo
+.section foo,"ao",@progbits,.text.f1,unique,1
+.quad 1
+
+// CHECK: foo
+.section foo,"ao",@progbits,.text.f2,unique,2
+.quad 2