你不应该在gui应用程序中使用while True或time.sleep，这两个过程都会导致gui冻结，迫使你使用像window.update()这样不必要的方法。
您的while True循环也可以使用预定的回调来轻松实现，这将允许您调用mainloop方法，以便您可以真正地将控制权交给GUI。
您还应该学习使用classes，以避免处理容易出错且难以读取的全局变量。
为了回答你的问题，你可以在更新绘图的同时继续保持gui的运行，一种方法是在一个单独的线程中运行绘图。
例如：

import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from tkinter import *
from random import randint
import threading

class Thread(threading.Thread):

    def __init__(self, window):
        super().__init__()
        self.window = window

    def animate(self, i):
        plt.cla()
        plt.plot(window.numberofsquares_list, window.time_list)

    def run(self): 
        # the run method gets automatically triggered when you start the thread
        FuncAnimation(plt.gcf(), self.animate, interval=3000)
        plt.tight_layout()
        plt.show()

class Window(Tk):  # the window class is your window
    # the __init__ method is essentially the same as your create window function
    def __init__(self, color, title, width, height):  
        super().__init__()  
        self.square_id = []  # make all your global variables class attributes
        self.numberofsquares = 0
        self.numberofsquares_list = []
        self.time = 0
        self.time_list = []
        self.height = height
        self.width  = width
        self.title(title)
        self.c = Canvas (self, width=width, height=height, bg=color)
        self.c.pack()
        self.create_squares()   # run the create squares at the end

    def create_squares(self):  
        # combined your create_squares function and your while loop into a single method
        self.time_list.append(self.time)  
        self.time = self.time + 1
        for _ in range(1, randint(1,20)):
            self.numberofsquares += 1
            x = randint(0, self.height)
            y = randint(0, self.width)
            square = self.c.create_rectangle(0,0,30, 30, fill='red')
            self.square_id.append(square)
            self.c.move(square, x, y)
        self.numberofsquares_list.append(self.numberofsquares)
        # this reschedules the function to run again at a random interval 
        # between half a second and 2 seconds
        self.after(randint(500,2000), self.create_squares)  

if __name__ == "__main__":
    window = Window('white', 'test', 500, 500)  # create the window
    thread = Thread(window)   # create the thread passing the window as argument
    thread.start()            # start the thread
    window.mainloop()         # run the gui event loop