If you would like to upload a complete structure of folders and subfolders on Sharepoint Online you can do it using Powershell and CSOM, using the following script.

You need to know:

- the URL of the site-collection ( looks like: https://tenant.sharepoint.com )

- the relative path of the destination site ( looks like: /sites/subsite_name )

- the library's name where the files will be uploaded

Attention to the subfolders structure to not exceed the maximum URL length permitted in Sharepoint Online.


This script can be useful to update a specific field on a library located on a Sharepoint Online tenant
You need to know 5 mandatory parameters:
    - url_sharepoint         : the URL for root site collection
    - library                : the name of the destination library
    - url_site               : the relative path of the site
This script can be used as it is or can be changed based on your needs. For more details please feel free to contact me
Romeo Donca, February 2017
[Parameter(Mandatory=$true,HelpMessage="The root site collection URL")][string]$url_sharepoint,
[Parameter(Mandatory=$true,HelpMessage="The relative path for the site site URL ___ /sites/subsite")][string]$url_site,
[Parameter(Mandatory=$true,HelpMessage="The name for the library")][string]$library
$t1  = get-date
$source_folder = ((new-object -com Shell.Application).BrowseForFolder(0, "Select the source folder", 0, "")).Self.Path
$url = $url_sharepoint+$Url_site

Add-Type -Path "your_path\Microsoft.SharePoint.Client.dll"
Add-Type -Path "your_path\Microsoft.SharePoint.Client.Runtime.dll"
Import-Module MSOnline
$global:cred1 = Get-Credential
$clientContext = New-Object Microsoft.SharePoint.Client.ClientContext($url)
$cred = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($cred1.username, $cred1.Password) 
$clientContext.Credentials = $cred
$web = $clientContext.Web
$mylist = $web.GetList($url+"/"+$library)
###################### get folders existing  in the SOURCE
$directories= @()
foreach ($file in (Get-ChildItem  -Recurse -Path $source_folder -Attributes Directory))
    $directories +=($file.FullName.ToLower()).replace($source_folder.ToLower()+'\','')
foreach ($directory in $directories)
    $myfolder = $mylist.RootFolder
    $myfolder = $myfolder.Folders.Add($directory.split('\')[0])
    for ($i = 1; $i -le ($directory.split('\').Count-1) ; $i++)
        $myfolder = $myfolder.folders.Add(($directory.split('\'))[$i])
$t1  = get-date
$count = ((Get-ChildItem -File  -Recurse -Path $source_folder) | Measure-Object -Property FullName ).Count
foreach ($file in (Get-ChildItem -File  -Recurse -Path $source_folder))
    $t01  = get-date
    $url_dest = $url_sharepoint+$Url_site+'/'+$library+(($file.FullName.ToLower()).Replace($source_folder.ToLower(),'')).Replace('\','/')
    $FileStream = New-Object IO.FileStream($File.FullName,[System.IO.FileMode]::Open)
    $FileCreationInfo = New-Object Microsoft.SharePoint.Client.FileCreationInformation
    $FileCreationInfo.Overwrite = $true
    $FileCreationInfo.ContentStream = $FileStream
    $FileCreationInfo.URL = $url_dest
    $Upload = $mylist.RootFolder.Files.Add($FileCreationInfo)
    $listItem = $upload.ListItemAllFields
    Write-Host " Uploading file $i/$count $url_dest"
    $t02  = get-date
    $speed ="{0:n2}" -f ($file.Length/($t02-$t01).TotalSeconds/1mb)
    Write-Host "...................upload speed was " $speed " MB/sec"
$size = "{0:n2}" -f (gci -path $source_folder -recurse | measure-object -property length -sum).sum
$speed ="{0:n2}" -f ($size/($t2-$t1).TotalSeconds/1mb)
Write-Host "Medium upload speed was " $speed " MB/sec"